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abhimanyu12
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dpyd-classifier

pharmacogenomics
DPYD
variant-classification
population-genomics
South-Asian
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  1. README.md +27 -0
  2. data/clinvar_dpyd.tsv +597 -0
  3. data/cpic_dpyd_function.csv +14 -0
  4. data/gnomad_dpyd_sas.csv +121 -0
  5. data/inference_set.csv +324 -0
  6. data/training_data.csv +274 -0
  7. requirements.txt +10 -0
  8. run.sh +29 -0
  9. src/features.py +141 -0
  10. src/fetch_gnomad.py +116 -0
  11. src/gcs_io.py +26 -0
  12. src/infer.py +146 -0
  13. src/train.py +165 -0
  14. v1/models/lgbm_model.pkl +3 -0
  15. v1/models/rf_model.pkl +3 -0
  16. v1/models/xgb_model.pkl +3 -0
  17. v1/results/cv_metrics.json +74 -0
  18. v1/results/scaria_variant_rankings.csv +26 -0
  19. v1/training_data.csv +274 -0
  20. v2/models/lgbm_model.pkl +3 -0
  21. v2/models/rf_model.pkl +3 -0
  22. v2/models/xgb_model.pkl +3 -0
  23. v2/results/cv_metrics.json +74 -0
  24. v2/results/cv_metrics_v2.json +84 -0
  25. v2/results/scaria_variant_rankings.csv +26 -0
  26. v3/models/lgbm_model.pkl +3 -0
  27. v3/models/rf_model.pkl +3 -0
  28. v3/models/xgb_model.pkl +3 -0
  29. v3/results/cv_metrics.json +74 -0
  30. v3/results/cv_metrics_v2.json +84 -0
  31. v3/results/cv_metrics_v3.json +89 -0
  32. v3/results/scaria_variant_rankings.csv +26 -0
  33. v3/results/scaria_variant_rankings_v2.csv +26 -0
  34. v3/results/scaria_variant_rankings_v3.csv +26 -0
README.md ADDED
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+ ---
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+ license: apache-2.0
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+ tags:
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+ - pharmacogenomics
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+ - DPYD
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+ - variant-classification
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+ - population-genomics
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+ - South-Asian
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+ ---
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+
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+ # DPYD Variant Pathogenicity Classifier
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+
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+ Trained classifier for DPYD variant functional classification (no_function / decreased_function / normal_function) built by [Anukriti AI](https://anukritiai.com).
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+
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+ ## Versions
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+ - v1: Baseline — 273 training rows, 4 decreased_function examples, F1=0.0 for decreased_function
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+ - v2: +Offer 2014 + PharmVar data, SMOTE, domain features — 392 rows, 23 decreased_function examples, F1=0.66 (XGB)
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+ - v3: +AlphaMissense + CADD + VEP annotations on training set — AM importance 0→0.01, sentinel gap closed
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+
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+ ## Two-tier inference note
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+ For novel population-discovery variants without ClinVar significance or measured activity (e.g. Scaria 2025 Indian cohort), use AlphaMissense direct score rather than this classifier. The classifier is optimized for variants with clinical labels and measured activity data. See [validation paper](https://doi.org/10.5281/zenodo.20727790).
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+
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+ ## Ground truth sources
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+ PharmVar activity scores, Offer et al. 2014, GeT-RM 2024 (Gaedigk et al.), ClinVar
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+
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+ ## Citation
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+ Abhimanyu R B et al. "Deterministic, Population-Aware Pharmacogenomics Screening." Zenodo. https://doi.org/10.5281/zenodo.20727790
data/clinvar_dpyd.tsv ADDED
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1
+ chrom pos ref alt rsid clnsig geneinfo mc clnvc variation_id
2
+ 1 97078992 A G rs770320798 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3085646
3
+ 1 97078993 C G Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4071714
4
+ 1 97079002 G C rs956842768 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1799278
5
+ 1 97079005 C T rs140114515 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1799224
6
+ 1 97079012 CTT C rs1557849648 Uncertain_significance DPYD:1806 SO:0001589|frameshift_variant Deletion 2429122
7
+ 1 97079020 C A rs761584058 Uncertain_significance DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 1677117
8
+ 1 97079022 T TA rs1459699844 Uncertain_significance DPYD:1806 SO:0001589|frameshift_variant Duplication 555831
9
+ 1 97079056 C T rs151074666 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1050568
10
+ 1 97079060 A G rs1465795668 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 2638935
11
+ 1 97079062 T C rs745982505 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2204228
12
+ 1 97079067 C T rs672601273 not_provided DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100070
13
+ 1 97079071 C A rs1801268 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 635267
14
+ 1 97079073 C G Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3351245
15
+ 1 97079076 A C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3768464
16
+ 1 97079078 A G rs2524010261 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1878270
17
+ 1 97079079 C T rs2101548857 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1314377
18
+ 1 97079104 C T rs760235888 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1798056
19
+ 1 97079106 G A rs61757362 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2561299
20
+ 1 97079133 T A rs72547602 Pathogenic DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 433
21
+ 1 97079134 C A DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4491154
22
+ 1 97079139 T C rs145529148 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 715550
23
+ 1 97079147 C T rs1553209268 Uncertain_significance DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 552960
24
+ 1 97079204 C G rs17116357 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1232963
25
+ 1 97079215 T C rs290855 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1222833
26
+ 1 97079354 T C rs76665493 Likely_benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1200576
27
+ 1 97082265 G A DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4491159
28
+ 1 97082275 G A rs290854 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1255090
29
+ 1 97082321 G C rs375990495 Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 2429123
30
+ 1 97082329 C G rs2101557799 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 2674944
31
+ 1 97082345 A C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3505086
32
+ 1 97082351 G A Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 3571928
33
+ 1 97082365 T C rs141044036 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 551659
34
+ 1 97082367 C A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3505091
35
+ 1 97082373 T C rs762779297 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2368190
36
+ 1 97082389 C T rs763862486 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2622839
37
+ 1 97082391 T A rs67376798 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 88974
38
+ 1 97082394 A G rs372307932 Likely_pathogenic DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2581397
39
+ 1 97082397 A G rs2101558314 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1796716
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+ 1 97082400 GC G rs2524026293 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 2674948
41
+ 1 97082404 C CA rs2524026345 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Duplication 2674918
42
+ 1 97082415 A G rs748639205 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 558312
43
+ 1 97082430 C T rs1649223892 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 876926
44
+ 1 97082435 T A Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 3505087
45
+ 1 97082449 G A rs2101558812 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 3241364
46
+ 1 97082460 C T Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3364660
47
+ 1 97082471 C T rs377221676 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 429794
48
+ 1 97082472 T A DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 4491178
49
+ 1 97082803 C T rs2171826 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1269305
50
+ 1 97098470 T C rs375268978 Benign DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 100071
51
+ 1 97098485 T A DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 4491187
52
+ 1 97098488 C T rs1355754530 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001575|splice_donor_variant single_nucleotide_variant 2674904
53
+ 1 97098497 T G rs886046575 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 298280
54
+ 1 97098500 GA G rs1057516894 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Deletion 370956
55
+ 1 97098502 A G Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 4244655
56
+ 1 97098506 GC G rs1057517230 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Deletion 371384
57
+ 1 97098508 CT C rs778614771 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Deletion 1722331
58
+ 1 97098521 AAC A rs1650431372 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Deletion 2674914
59
+ 1 97098533 T A rs1553212596 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001587|nonsense single_nucleotide_variant 550624
60
+ 1 97098550 A G rs2524093994 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 2236534
61
+ 1 97098575 T A rs1057516873 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001587|nonsense single_nucleotide_variant 370928
62
+ 1 97098577 T C Conflicting_classifications_of_pathogenicity DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3339417
63
+ 1 97098581 C A rs2524094119 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001587|nonsense single_nucleotide_variant 2674908
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+ 1 97098582 T C Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 3353132
65
+ 1 97098598 C T rs1801267 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 437
66
+ 1 97098601 T C rs2524094303 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 2453342
67
+ 1 97098602 G A rs771839581 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001587|nonsense single_nucleotide_variant 2674942
68
+ 1 97098605 C A rs2524094344 Pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001587|nonsense single_nucleotide_variant 1805301
69
+ 1 97098609 A G rs773002572 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 3230331
70
+ 1 97098616 C A Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3777723
71
+ 1 97098621 A C rs919596571 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 874134
72
+ 1 97098623 T C rs762911226 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 298281
73
+ 1 97098632 T G Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3273700
74
+ 1 97098640 G A rs1570451084 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 764540
75
+ 1 97192771 C A DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 4491206
76
+ 1 97192839 C T rs4950023 Benign DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 1267185
77
+ 1 97193067 A C DPYD:1806|DPYD-AS1:100873932 SO:0001575|splice_donor_variant single_nucleotide_variant 4491226
78
+ 1 97193067 A G DPYD:1806|DPYD-AS1:100873932 SO:0001575|splice_donor_variant single_nucleotide_variant 4491235
79
+ 1 97193068 C T rs1057517095 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001575|splice_donor_variant single_nucleotide_variant 371215
80
+ 1 97193072 G C Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 4014738
81
+ 1 97193091 C T Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3505083
82
+ 1 97193092 G A rs557220418 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 585802
83
+ 1 97193093 T C rs672601274 not_provided DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 100072
84
+ 1 97193098 C A rs773815814 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 2567626
85
+ 1 97193101 G GT rs1057517327 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Duplication 371510
86
+ 1 97193105 C T rs903875506 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 3230330
87
+ 1 97193106 C A DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 4491245
88
+ 1 97193111 CT C rs746991079 Pathogenic/Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Deletion 551707
89
+ 1 97193124 G A rs752228747 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 2346770
90
+ 1 97193127 G C rs1031125025 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 593062
91
+ 1 97193137 G A rs1057517271 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001587|nonsense single_nucleotide_variant 371437
92
+ 1 97193138 T C Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 4825331
93
+ 1 97193141 A G rs777542103 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 3230329
94
+ 1 97193142 T C Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 4244654
95
+ 1 97193142 TC T rs2524554561 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Deletion 3241362
96
+ 1 97193143 C T Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 4617950
97
+ 1 97193159 T C rs672601275 not_provided DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 100073
98
+ 1 97193163 A G rs571114616 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 451401
99
+ 1 97193166 C A rs886046576 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 298282
100
+ 1 97193197 T C rs1218404593 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 1206180
101
+ 1 97193201 G T rs1337420489 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001587|nonsense single_nucleotide_variant 3241360
102
+ 1 97193206 C T rs199777072 Conflicting_classifications_of_pathogenicity DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 1343425
103
+ 1 97193317 T C DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 4491255
104
+ 1 97234569 C T rs11808108 Benign DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 1280876
105
+ 1 97234689 T C rs17432999 Benign DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 1241217
106
+ 1 97234773 A AT rs544905665 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant Duplication 1212885
107
+ 1 97234847 A G Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 3340003
108
+ 1 97234851 C A Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001575|splice_donor_variant single_nucleotide_variant 4796658
109
+ 1 97234851 C G rs1252510761 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001575|splice_donor_variant single_nucleotide_variant 2674917
110
+ 1 97234854 G A rs2524774440 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001587|nonsense single_nucleotide_variant 3241369
111
+ 1 97234871 C T Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 4014740
112
+ 1 97234873 A G rs55725052 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 3230328
113
+ 1 97234878 G T rs1241910237 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3230327
114
+ 1 97234902 A C Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 4617949
115
+ 1 97234916 G A rs547099198 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 558527
116
+ 1 97234937 G T rs777673186 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 976091
117
+ 1 97234946 C A Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 4617948
118
+ 1 97234947 G A rs770958862 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3252435
119
+ 1 97234954 GGA G rs1162905063 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Deletion 2674910
120
+ 1 97234956 AGGT GC rs1057516510 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Indel 370465
121
+ 1 97234959 T C rs1365638731 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 2587443
122
+ 1 97234965 C A rs672601276 not_provided DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 100074
123
+ 1 97234974 C T rs1304906107 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 1789580
124
+ 1 97234980 G T rs2524775725 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3085645
125
+ 1 97234986 T C Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3842365
126
+ 1 97234991 G T rs56005131 drug_response DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 287480
127
+ 1 97234993 C A rs672601277 not_provided DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 100075
128
+ 1 97234995 C G Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001574|splice_acceptor_variant single_nucleotide_variant 3342367
129
+ 1 97235033 C T rs12137711 Benign DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 100076
130
+ 1 97235034 C A rs672601278 not_provided DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 100077
131
+ 1 97235103 A G rs672601279 not_provided DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 100078
132
+ 1 97305159 G A rs34534958 not_provided DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 100079
133
+ 1 97305252 C T rs369672458 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 774156
134
+ 1 97305258 C T rs2101035489 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001575|splice_donor_variant single_nucleotide_variant 2674923
135
+ 1 97305271 C CT rs1057516828 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Insertion 370868
136
+ 1 97305275 T C Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 3273698
137
+ 1 97305275 T G rs772853110 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 1788965
138
+ 1 97305277 T C Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3842362
139
+ 1 97305279 G A rs112766203 Conflicting_classifications_of_pathogenicity DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 874135
140
+ 1 97305282 C T rs267598786 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 73995
141
+ 1 97305283 G A rs759372918 Pathogenic/Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001587|nonsense single_nucleotide_variant 370760
142
+ 1 97305289 C G rs2101035792 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 2231956
143
+ 1 97305291 A G Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3842363
144
+ 1 97305316 C T Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3505094
145
+ 1 97305335 C G rs1397691452 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 2638936
146
+ 1 97305348 GT G rs1558014211 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Deletion 3241368
147
+ 1 97305351 T TTGGTG Pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Duplication 4081632
148
+ 1 97305363 A C Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3352671
149
+ 1 97305364 C T rs1801160 drug_response DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 100080
150
+ 1 97305365 G A rs139543981 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001819|synonymous_variant single_nucleotide_variant 298283
151
+ 1 97305372 G A rs146529561 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 298284
152
+ 1 97305375 C A rs2101036846 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 1805513
153
+ 1 97305376 C T Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 3842359
154
+ 1 97305381 A G rs74104343 Benign/Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 735872
155
+ 1 97305389 C T rs377136032 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 298285
156
+ 1 97305422 A G rs672601280 not_provided DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 100081
157
+ 1 97305449 C G DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 4491356
158
+ 1 97306171 T A DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 4491367
159
+ 1 97306173 T C rs746718279 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 680898
160
+ 1 97306175 ACCTT A rs1553251903 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001575|splice_donor_variant Microsatellite 554975
161
+ 1 97306176 C CCTT Uncertain_significance DPYD:1806|DPYD-AS1:100873932 Duplication 3907178
162
+ 1 97306176 C T Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001575|splice_donor_variant single_nucleotide_variant 4081350
163
+ 1 97306177 C A DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 4491376
164
+ 1 97306177 CT C rs1553251907 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant Deletion 551164
165
+ 1 97306188 G C rs1553251908 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant single_nucleotide_variant 551004
166
+ 1 97306195 C T rs145548112 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 100082
167
+ 1 97306208 A T rs1399492718 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 2567627
168
+ 1 97306209 TC T rs2525218019 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant;SO:0001619|non-coding_transcript_variant Deletion 2674938
169
+ 1 97306210 CA C rs1165702486 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant;SO:0001619|non-coding_transcript_variant Deletion 3241365
170
+ 1 97306220 TG T rs1064796552 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001589|frameshift_variant;SO:0001619|non-coding_transcript_variant Deletion 423651
171
+ 1 97306240 A T Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 4244653
172
+ 1 97306241 A T rs753891721 Likely_benign DPYD:1806|DPYD-AS1:100873932 SO:0001619|non-coding_transcript_variant;SO:0001819|synonymous_variant single_nucleotide_variant 1786173
173
+ 1 97306246 T A Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 3505089
174
+ 1 97306265 C T rs753296078 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001587|nonsense;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 2674925
175
+ 1 97306269 C T Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 4680892
176
+ 1 97306272 C A rs1336020354 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 875065
177
+ 1 97306276 T C rs756890859 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 3085643
178
+ 1 97306281 C A rs375436137 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 2521331
179
+ 1 97306281 C T rs375436137 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 2412214
180
+ 1 97306282 G A rs538703919 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 804762
181
+ 1 97306285 C A rs202212118 Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 298286
182
+ 1 97306288 G C Uncertain_significance DPYD:1806|DPYD-AS1:100873932 SO:0001583|missense_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 4014742
183
+ 1 97306291 C A rs1667161380 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001587|nonsense;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 2674932
184
+ 1 97306298 C A rs2525218826 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001574|splice_acceptor_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 2674916
185
+ 1 97306299 T C rs2525218835 Likely_pathogenic DPYD:1806|DPYD-AS1:100873932 SO:0001574|splice_acceptor_variant;SO:0001619|non-coding_transcript_variant single_nucleotide_variant 2674945
186
+ 1 97306391 C A rs7556439 Benign DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 1270293
187
+ 1 97306519 A G DPYD:1806|DPYD-AS1:100873932 SO:0001627|intron_variant single_nucleotide_variant 4491386
188
+ 1 97373297 G A rs74105115 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1260675
189
+ 1 97373298 C T rs55652347 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1249429
190
+ 1 97373331 T C rs11582179 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1222617
191
+ 1 97373404 C T rs115139529 Likely_benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1204776
192
+ 1 97373416 A G rs1879374 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1266890
193
+ 1 97373460 A G rs1890138 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1228303
194
+ 1 97373519 T C rs368002831 not_provided DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100083
195
+ 1 97373560 C G rs769167857 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 370923
196
+ 1 97373560 CCTGCCCACAGGCCAGG C rs773499329 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 188871
197
+ 1 97373570 G C rs183475941 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 100084
198
+ 1 97373572 C T rs2525630867 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1784995
199
+ 1 97373579 C CA rs1057517396 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Duplication 371596
200
+ 1 97373592 C G Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4244661
201
+ 1 97373596 T C rs763506271 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3230325
202
+ 1 97373615 AT A rs1057517055 Pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 371160
203
+ 1 97373629 C A rs138545885 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1256250
204
+ 1 97373635 C T rs1671426656 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2268284
205
+ 1 97373635 CTCCAGAA C rs1440380546 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant Deletion 813354
206
+ 1 97373644 C G Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3273701
207
+ 1 97373645 C A DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 4491784
208
+ 1 97373857 C G rs6699630 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1286217
209
+ 1 97382318 T C rs72728438 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100086
210
+ 1 97382392 C T rs772254904 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 450621
211
+ 1 97382396 AG A rs1057516710 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 370712
212
+ 1 97382428 T C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4687807
213
+ 1 97382430 T C rs780120302 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2397850
214
+ 1 97382432 G T rs1570632355 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 2674953
215
+ 1 97382442 A G rs2101564724 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1209996
216
+ 1 97382452 C A rs2525684263 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3085642
217
+ 1 97382460 A G rs1346856479 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2587441
218
+ 1 97382461 T G rs55971861 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1782389
219
+ 1 97382485 T G rs12078940 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1280222
220
+ 1 97382584 G T rs56279424 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1232655
221
+ 1 97450042 T C rs369990607 Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1806168
222
+ 1 97450053 A T Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 3375110
223
+ 1 97450054 C T Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4685698
224
+ 1 97450056 T TA rs760156122 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant Duplication 2674929
225
+ 1 97450058 C A DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 4492049
226
+ 1 97450058 C G rs3918290 Pathogenic/Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 2429124
227
+ 1 97450058 C T rs3918290 drug_response DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 432
228
+ 1 97450059 G A rs3918289 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 100087
229
+ 1 97450065 TG T rs72549303 drug_response DPYD:1806 SO:0001589|frameshift_variant Deletion 635266
230
+ 1 97450067 GA G rs2523871765 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 3241357
231
+ 1 97450068 A G rs17376848 drug_response DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 100088
232
+ 1 97450099 C T Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3337051
233
+ 1 97450101 C T rs1057516388 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 370307
234
+ 1 97450107 T G Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 3842358
235
+ 1 97450114 G A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3340231
236
+ 1 97450133 C A rs1057516671 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 370668
237
+ 1 97450142 GAA G Pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 4081633
238
+ 1 97450144 A G rs1676330398 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2485396
239
+ 1 97450168 A G rs147601618 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 550673
240
+ 1 97450183 GT G rs2523873242 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 2674915
241
+ 1 97450189 C T rs138616379 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 554703
242
+ 1 97450190 G A rs59086055 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 282919
243
+ 1 97450193 T TGA Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Duplication 4081349
244
+ 1 97450199 TG T rs1346124437 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 632121
245
+ 1 97450207 A G rs374527058 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1805235
246
+ 1 97450220 T C rs889910324 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2453343
247
+ 1 97450233 G C DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4492331
248
+ 1 97450288 G A rs672601281 not_provided DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100089
249
+ 1 97515585 A AT rs56080540 Benign DPYD:1806 SO:0001627|intron_variant Insertion 1225056
250
+ 1 97515643 T TA rs145228578 Benign DPYD:1806 SO:0001627|intron_variant Duplication 1259760
251
+ 1 97515686 T C rs2811178 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100090
252
+ 1 97515687 G A rs2786783 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100091
253
+ 1 97515733 A G rs778754188 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 875994
254
+ 1 97515737 A C rs2524204644 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2486730
255
+ 1 97515738 G C rs886553467 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1778899
256
+ 1 97515738 GA G rs764584080 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 370256
257
+ 1 97515748 G T Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4014739
258
+ 1 97515749 T G Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4244657
259
+ 1 97515751 A AG rs1290522460 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Duplication 2674931
260
+ 1 97515763 C T rs2101975422 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 3241366
261
+ 1 97515765 T A rs148372305 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 738289
262
+ 1 97515766 C T rs1188134745 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3233733
263
+ 1 97515783 T G rs1648178154 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1777949
264
+ 1 97515785 G A rs1057516968 Pathogenic/Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 371053
265
+ 1 97515787 A C rs55886062 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 88975
266
+ 1 97515791 T C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3505093
267
+ 1 97515794 AT A rs1057517018 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 371114
268
+ 1 97515795 T C rs780421257 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1777694
269
+ 1 97515796 G A rs754125729 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2524151
270
+ 1 97515812 T C rs771648776 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 585801
271
+ 1 97515815 C A DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4492888
272
+ 1 97515815 C T rs777425216 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 298287
273
+ 1 97515816 G A rs149101842 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1777250
274
+ 1 97515839 T C rs1801159 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100092
275
+ 1 97515849 T C rs762029458 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 2638937
276
+ 1 97515851 C T rs142619737 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100093
277
+ 1 97515852 G A rs760853559 Uncertain_significance DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 298288
278
+ 1 97515855 CATTTCTACACT C rs2524206318 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 3241361
279
+ 1 97515857 T G Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4617944
280
+ 1 97515864 A G rs1257539978 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 2567625
281
+ 1 97515865 C T rs1801158 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100094
282
+ 1 97515886 G A rs886046577 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 298289
283
+ 1 97515891 G C rs752329473 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 2674912
284
+ 1 97515892 TAAAAGA GT rs2524206768 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Indel 3241367
285
+ 1 97515901 G A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3505095
286
+ 1 97515904 A G Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4617951
287
+ 1 97515911 G A rs672601282 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100095
288
+ 1 97515912 C T rs369465750 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 2587442
289
+ 1 97515913 T C DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4492893
290
+ 1 97515923 C T rs148994843 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1327419
291
+ 1 97515928 G A rs760663364 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 558310
292
+ 1 97515928 G C rs760663364 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 298290
293
+ 1 97515929 C G rs1648195326 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2501031
294
+ 1 97515942 C G rs766535034 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 2674949
295
+ 1 97515943 T C rs2524207205 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 2674926
296
+ 1 97515950 T C rs56056384 Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 298291
297
+ 1 97515952 C T rs55699321 Benign/Likely_benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 298292
298
+ 1 97515958 A T DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4492902
299
+ 1 97516031 C T rs6657204 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1274398
300
+ 1 97516066 G GA rs141050810 Benign DPYD:1806 SO:0001627|intron_variant Duplication 1245965
301
+ 1 97516150 C A DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4492928
302
+ 1 97516150 C T rs1337752 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1282683
303
+ 1 97549360 G A DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4492953
304
+ 1 97549384 C A rs2786525 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1239321
305
+ 1 97549485 T C DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4492990
306
+ 1 97549544 G T rs199469537 Likely_benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100096
307
+ 1 97549554 G C Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4847504
308
+ 1 97549559 C T rs1057517126 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 371253
309
+ 1 97549560 C T rs775930761 Uncertain_significance DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 2391206
310
+ 1 97549564 A G rs2524372985 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3239416
311
+ 1 97549565 C T rs138391898 Likely_benign DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2567628
312
+ 1 97549565 CG C rs1057516615 Likely_pathogenic DPYD:1806 SO:0001587|nonsense Deletion 370593
313
+ 1 97549582 C T rs1214305633 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 2674954
314
+ 1 97549590 T A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3390792
315
+ 1 97549590 T C rs116364703 Benign/Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 711962
316
+ 1 97549592 G A rs1382838576 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 3241355
317
+ 1 97549609 G A rs72549304 Pathogenic/Likely_pathogenic DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 298293
318
+ 1 97549612 T A rs1264198400 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3069130
319
+ 1 97549640 C T rs1221109314 Likely_benign DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2235853
320
+ 1 97549647 A G Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 4244652
321
+ 1 97549669 C T rs776082092 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 521319
322
+ 1 97549676 G A rs2524373926 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 2634691
323
+ 1 97549679 T A rs2524373962 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3085639
324
+ 1 97549687 G A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4843747
325
+ 1 97549694 C T rs912917991 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2238929
326
+ 1 97549695 TTCTGGGAGACCCCA T rs757940841 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 2674906
327
+ 1 97549697 CT C rs1437370264 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 2674939
328
+ 1 97549701 G A rs2524374167 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1771336
329
+ 1 97549704 A AC rs779948148 Pathogenic/Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Duplication 371469
330
+ 1 97549713 G A rs57918000 Benign/Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 100097
331
+ 1 97549715 T C rs750147471 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 876976
332
+ 1 97549723 A ATAGGGCTC rs2524374326 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Duplication 2674901
333
+ 1 97549726 G C rs144395748 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100098
334
+ 1 97549729 C T rs1557791062 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3230324
335
+ 1 97549735 G A rs72975710 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 876977
336
+ 1 97549735 G C rs72975710 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 298294
337
+ 1 97549740 T C DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 4493000
338
+ 1 97549745 C T rs1435774234 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 3241358
339
+ 1 97549746 T C rs1057516713 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 370715
340
+ 1 97549746 T G rs1057516713 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 2633588
341
+ 1 97549747 G C rs193920862 Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 161459
342
+ 1 97549758 T G rs886046578 Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 298295
343
+ 1 97549850 A T rs61789183 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100099
344
+ 1 97549863 T C DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4493010
345
+ 1 97549925 G T rs2811162 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1289519
346
+ 1 97573759 C A rs1057516357 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 370261
347
+ 1 97573760 C A DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4493057
348
+ 1 97573762 T G rs200709381 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 876978
349
+ 1 97573765 G C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4244656
350
+ 1 97573782 AC A rs1057516761 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 370780
351
+ 1 97573787 AG A rs1057517189 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 371335
352
+ 1 97573788 G A rs780469489 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1769673
353
+ 1 97573789 G A rs1290815802 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 585800
354
+ 1 97573796 TG T rs2523608314 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 2674930
355
+ 1 97573804 T C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4244658
356
+ 1 97573806 G A rs770549765 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1769161
357
+ 1 97573819 A G rs200693895 Likely_benign DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1677165
358
+ 1 97573821 C A rs764666241 Likely_benign DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2520613
359
+ 1 97573826 G C rs1165667490 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2484175
360
+ 1 97573834 T C rs757155354 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3085638
361
+ 1 97573856 C A rs755031341 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 489080
362
+ 1 97573858 T A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4014743
363
+ 1 97573862 G A DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 4493067
364
+ 1 97573863 C T rs56038477 drug_response DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 100100
365
+ 1 97573870 C T rs199646142 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 874187
366
+ 1 97573871 G A rs528430685 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 874188
367
+ 1 97573879 T C rs886046579 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 298296
368
+ 1 97573881 C T rs61622928 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100101
369
+ 1 97573886 C A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3505096
370
+ 1 97573919 G A rs140602333 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 585799
371
+ 1 97573919 G T Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 3505084
372
+ 1 97573920 TG T rs1553197926 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 557959
373
+ 1 97573932 T C rs753482702 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1738409
374
+ 1 97573942 TCA T rs769925158 Likely_pathogenic DPYD:1806 SO:0001587|nonsense Microsatellite 1723398
375
+ 1 97573943 C A rs78060119 drug_response DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 1032887
376
+ 1 97573951 T A DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4493075
377
+ 1 97573959 A G rs150759598 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 2561298
378
+ 1 97573960 G C rs1354585423 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 973462
379
+ 1 97573970 T C rs144935781 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 985228
380
+ 1 97573981 A C rs672601283 not_provided DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100102
381
+ 1 97573985 A G rs56293913 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100103
382
+ 1 97579893 G C rs75017182 drug_response DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 635263
383
+ 1 97592953 A C DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4493097
384
+ 1 97593057 C T rs74105265 Likely_benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1190797
385
+ 1 97593217 C G Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 3370431
386
+ 1 97593221 C T Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 3842360
387
+ 1 97593224 AG A rs1553201443 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 553633
388
+ 1 97593229 C T Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3842364
389
+ 1 97593235 TTA T rs749571474 Pathogenic/Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Microsatellite 370309
390
+ 1 97593238 T C rs72549305 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 552935
391
+ 1 97593274 G A rs779557503 Likely_pathogenic DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2664661
392
+ 1 97593276 C T rs377143350 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 551494
393
+ 1 97593292 G C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3571973
394
+ 1 97593298 A G rs771885007 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 298297
395
+ 1 97593303 GCA G rs1553201476 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Microsatellite 558704
396
+ 1 97593310 C CA rs1654652414 Likely_pathogenic DPYD:1806 SO:0001587|nonsense Duplication 2674933
397
+ 1 97593315 G A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3774071
398
+ 1 97593319 T A rs886046580 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 298298
399
+ 1 97593322 C T rs183385770 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 550741
400
+ 1 97593326 A C rs774390439 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 3025321
401
+ 1 97593343 C A rs72549306 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1327416
402
+ 1 97593351 C T rs747633945 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 298299
403
+ 1 97593352 G A rs757994597 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3085649
404
+ 1 97593352 G GT rs2523745739 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Duplication 2674921
405
+ 1 97593353 T C rs1260688429 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3085648
406
+ 1 97593357 G T DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 4493108
407
+ 1 97593370 A G rs770566506 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1804189
408
+ 1 97593379 C T rs201018345 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2573364
409
+ 1 97593380 G A rs768834079 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 3230334
410
+ 1 97593380 G T rs768834079 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 2674937
411
+ 1 97593389 T C rs577302209 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 2674947
412
+ 1 97593438 A C DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4493119
413
+ 1 97593438 A G rs115349832 not_provided DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100104
414
+ 1 97594913 C CT rs1397160848 Likely_benign DPYD:1806 SO:0001627|intron_variant Duplication 1197875
415
+ 1 97594925 A C rs2811202 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100105
416
+ 1 97595023 T C rs114968502 not_provided DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100106
417
+ 1 97595057 A G rs1654782224 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 2674936
418
+ 1 97595106 TA T rs1057516711 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 370713
419
+ 1 97595122 G A rs2102259303 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 1335974
420
+ 1 97595124 G A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4687804
421
+ 1 97595130 C T rs672601284 not_provided DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100107
422
+ 1 97595138 G A rs2523757968 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1764684
423
+ 1 97595140 T C rs779925747 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1764629
424
+ 1 97595145 T C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4014741
425
+ 1 97595148 T C rs672601285 not_provided DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100108
426
+ 1 97595149 T C rs146356975 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1328879
427
+ 1 97595166 C A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3902445
428
+ 1 97595167 C G rs1057516696 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 370698
429
+ 1 97595197 G A rs2786491 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100109
430
+ 1 97595421 T C rs3790386 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1232740
431
+ 1 97679005 A G rs672601286 not_provided DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100110
432
+ 1 97679054 A G rs112550271 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100111
433
+ 1 97679082 G A rs1660302424 Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 874189
434
+ 1 97679094 C A DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 4493213
435
+ 1 97679104 T C rs746329786 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2255373
436
+ 1 97679120 G A DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 4493222
437
+ 1 97679132 CA C rs1660305188 Pathogenic DPYD:1806 SO:0001587|nonsense Deletion 2674913
438
+ 1 97679138 G A Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 3777998
439
+ 1 97679155 T C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3505092
440
+ 1 97679170 T C rs45589337 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 235464
441
+ 1 97679173 C T rs141726921 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2634579
442
+ 1 97679174 G A rs754745863 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 3230333
443
+ 1 97679174 G T rs754745863 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 2674941
444
+ 1 97679175 C T rs764945792 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2207615
445
+ 1 97679177 A C rs556933127 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1760153
446
+ 1 97679183 C T rs2524268975 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 3241363
447
+ 1 97679184 T C rs1300669537 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 552475
448
+ 1 97679199 T C DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4493229
449
+ 1 97679300 T C rs3790387 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100112
450
+ 1 97691712 T A rs1033092437 Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 878396
451
+ 1 97691715 A G rs1057517065 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 371177
452
+ 1 97691717 C A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4847552
453
+ 1 97691736 A G rs2524346611 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3085647
454
+ 1 97691740 G A rs376128878 Uncertain_significance DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 878397
455
+ 1 97691742 T G Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3842357
456
+ 1 97691748 T G rs1185250556 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2581481
457
+ 1 97691753 A T Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3273697
458
+ 1 97691769 G A rs780025995 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1804875
459
+ 1 97691775 C T rs755416212 Likely_pathogenic DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 555616
460
+ 1 97691776 G A rs1801266 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 298300
461
+ 1 97691782 G A rs2524347160 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 2674924
462
+ 1 97691785 G T Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4244660
463
+ 1 97691806 G A rs74774246 Benign/Likely_benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 585804
464
+ 1 97692035 C T rs2786511 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1225146
465
+ 1 97699212 C T rs6668296 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1288056
466
+ 1 97699345 C G Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4847508
467
+ 1 97699350 C A rs867460475 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 2674940
468
+ 1 97699350 C T rs867460475 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 371334
469
+ 1 97699351 C T DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4493334
470
+ 1 97699370 C A rs146170505 Pathogenic/Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 370661
471
+ 1 97699373 G A rs1220608789 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 632791
472
+ 1 97699392 G A rs190048823 Uncertain_significance DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 878398
473
+ 1 97699399 T C rs72549307 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 554571
474
+ 1 97699403 C A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4617946
475
+ 1 97699408 C A rs376073289 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 806173
476
+ 1 97699408 C T rs376073289 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2506135
477
+ 1 97699409 G A rs1411354209 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 3241370
478
+ 1 97699413 CA C rs2524392157 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 2674955
479
+ 1 97699425 A G Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 3505085
480
+ 1 97699430 T G rs72549308 Likely_pathogenic DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2674903
481
+ 1 97699440 A G rs758927521 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1750509
482
+ 1 97699440 A T rs758927521 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1750505
483
+ 1 97699455 AAG A rs2524392830 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Microsatellite 3241356
484
+ 1 97699461 A G rs149843476 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1749232
485
+ 1 97699474 T C rs115232898 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100113
486
+ 1 97699475 A C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3371628
487
+ 1 97699483 G C DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4493343
488
+ 1 97699486 A AT rs754785410 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Duplication 2674907
489
+ 1 97699486 A T rs779728902 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1321453
490
+ 1 97699489 T G rs672601287 not_provided DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100114
491
+ 1 97699506 C T rs6670886 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 100115
492
+ 1 97699507 GA G rs1057516997 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 371088
493
+ 1 97699511 G T Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4014735
494
+ 1 97699520 T A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3390790
495
+ 1 97699523 G A rs2100972370 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 2573026
496
+ 1 97699534 A G rs763061658 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2557246
497
+ 1 97699535 T C rs2297595 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100116
498
+ 1 97699542 G C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3390791
499
+ 1 97699548 C T rs2100972539 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 2674951
500
+ 1 97699549 T C rs928629166 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 2674922
501
+ 1 97699551 C T rs202011255 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 2364828
502
+ 1 97699552 G A rs767955683 Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1032889
503
+ 1 97699692 A T rs78682297 Likely_benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1189191
504
+ 1 97720673 T C rs55684412 Benign DPYD:1806 SO:0001624|3_prime_UTR_variant;SO:0001627|intron_variant single_nucleotide_variant 1286242
505
+ 1 97720861 C A Likely_benign DPYD:1806 SO:0001624|3_prime_UTR_variant;SO:0001627|intron_variant single_nucleotide_variant 3910105
506
+ 1 97720901 A G rs2524533594 Uncertain_significance DPYD:1806 SO:0001583|missense_variant;SO:0001627|intron_variant single_nucleotide_variant 2271780
507
+ 1 97720906 A T rs1349131310 Likely_benign DPYD:1806 SO:0001627|intron_variant;SO:0001819|synonymous_variant single_nucleotide_variant 3041744
508
+ 1 97720909 G C rs72977734 Benign DPYD:1806 SO:0001583|missense_variant;SO:0001627|intron_variant single_nucleotide_variant 585803
509
+ 1 97721231 G T rs79063448 Likely_benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 1198724
510
+ 1 97721492 C T rs56276561 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100117
511
+ 1 97721505 C T rs373218392 Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 878399
512
+ 1 97721509 C A rs1057516763 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 370782
513
+ 1 97721518 C A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4532748
514
+ 1 97721519 A G rs190771411 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 298301
515
+ 1 97721529 A T rs2101026231 Pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 1192270
516
+ 1 97721530 A G Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 4843748
517
+ 1 97721542 T C rs200562975 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 633188
518
+ 1 97721545 T C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4617943
519
+ 1 97721548 G GTCCC rs2524538529 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Duplication 2674909
520
+ 1 97721571 T C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4244659
521
+ 1 97721577 C T DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4493396
522
+ 1 97721626 C T rs778022685 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2302867
523
+ 1 97721640 GAA G rs2524539576 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Deletion 2674950
524
+ 1 97721648 C G rs377169736 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 452082
525
+ 1 97721651 C T rs370615432 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1731361
526
+ 1 97721653 T C rs2524539694 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2493169
527
+ 1 97721657 A C rs2524539741 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1730734
528
+ 1 97721665 A G rs1283205838 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2441031
529
+ 1 97721672 C G rs1057516356 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 370259
530
+ 1 97740377 T G rs370363977 Uncertain_significance DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 633189
531
+ 1 97740390 A G Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 3370432
532
+ 1 97740391 C T rs746368304 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 2439928
533
+ 1 97740410 GATGA G rs72549309 Pathogenic DPYD:1806 SO:0001589|frameshift_variant Microsatellite 495550
534
+ 1 97740434 A G rs2101070143 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 1694519
535
+ 1 97740439 G C rs143986398 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 804763
536
+ 1 97740441 C A rs928681171 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2635856
537
+ 1 97740444 C A rs672601288 not_provided DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 100118
538
+ 1 97740448 T A rs672601289 not_provided DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 100119
539
+ 1 97740450 T C Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3842361
540
+ 1 97740452 A G rs1056815262 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 2494416
541
+ 1 97740455 C T rs201841475 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 788079
542
+ 1 97740456 G A rs568132506 Pathogenic/Likely_pathogenic DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1028072
543
+ 1 97740501 T C DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4493400
544
+ 1 97740560 C T rs552156826 not_provided DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100120
545
+ 1 97828078 A G rs672601290 not_provided DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100121
546
+ 1 97828113 C A rs1553247675 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 554296
547
+ 1 97828115 T A rs776692894 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 370260
548
+ 1 97828116 C T Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4617947
549
+ 1 97828127 G A rs189768576 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 370757
550
+ 1 97828127 GGAGAGCT ATTG rs2525244930 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Indel 2674934
551
+ 1 97828129 A C rs762102298 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1787404
552
+ 1 97828138 C T rs767818267 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2606986
553
+ 1 97828139 G A rs141597515 Pathogenic/Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 370660
554
+ 1 97828142 C A rs2525245079 Pathogenic/Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 2674920
555
+ 1 97828153 G A rs371587702 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2387228
556
+ 1 97828158 C G rs2101479863 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2405034
557
+ 1 97828159 T G rs2101479885 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2405032
558
+ 1 97828160 T C rs367619008 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 553625
559
+ 1 97828162 A T rs2525245478 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2249226
560
+ 1 97828166 C G rs1557992438 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3085641
561
+ 1 97828169 C A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 4825332
562
+ 1 97828196 T G Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3505088
563
+ 1 97828198 T G rs1669337684 Pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant single_nucleotide_variant 1032888
564
+ 1 97828249 T A DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 4493437
565
+ 1 97828265 C T rs115632870 Benign DPYD:1806 SO:0001627|intron_variant single_nucleotide_variant 100122
566
+ 1 97883262 A T rs1057516405 Likely_pathogenic DPYD:1806 SO:0001575|splice_donor_variant single_nucleotide_variant 370330
567
+ 1 97883268 C A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3273696
568
+ 1 97883273 C A Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 3779287
569
+ 1 97883273 C T Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 4823300
570
+ 1 97883277 T G rs756684474 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2231768
571
+ 1 97883279 AGGATTTCT A rs1207177925 Pathogenic/Likely_pathogenic DPYD:1806 SO:0001587|nonsense Deletion 502676
572
+ 1 97883294 AT G rs2523808126 Likely_pathogenic DPYD:1806 SO:0001589|frameshift_variant Indel 2674928
573
+ 1 97883319 G T rs748974194 Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 2674946
574
+ 1 97883328 C T rs528768620 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 1302258
575
+ 1 97883329 A rs1801265 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0002073|no_sequence_alteration single_nucleotide_variant 100123
576
+ 1 97883329 A G rs1801265 drug_response DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 435
577
+ 1 97883341 G A rs775601164 Uncertain_significance DPYD:1806 SO:0001583|missense_variant single_nucleotide_variant 2474710
578
+ 1 97883353 G A rs72549310 Pathogenic/Likely_pathogenic DPYD:1806 SO:0001587|nonsense single_nucleotide_variant 188848
579
+ 1 97883366 C T rs763165014 Conflicting_classifications_of_pathogenicity DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 878990
580
+ 1 97883369 G T rs267598790 Likely_benign DPYD:1806 SO:0001819|synonymous_variant single_nucleotide_variant 550879
581
+ 1 97883371 TACTCTAAAG T rs1672325016 Likely_pathogenic DPYD:1806 SO:0001574|splice_acceptor_variant Deletion 2674905
582
+ 1 97920880 G C rs1439572087 Uncertain_significance DPYD:1806|LOC129930998:129930998 SO:0001627|intron_variant single_nucleotide_variant 2445788
583
+ 1 97920886 C T rs769820114 Uncertain_significance DPYD:1806|LOC129930998:129930998 SO:0001583|missense_variant single_nucleotide_variant 2508454
584
+ 1 97920887 G C rs376273539 Uncertain_significance DPYD:1806|LOC129930998:129930998 SO:0001583|missense_variant single_nucleotide_variant 1698665
585
+ 1 97920902 C T rs774730464 Likely_benign DPYD:1806|LOC129930998:129930998 SO:0001819|synonymous_variant single_nucleotide_variant 3230326
586
+ 1 97920910 G GC Pathogenic DPYD:1806|LOC129930998:129930998 SO:0001589|frameshift_variant Duplication 4536140
587
+ 1 97920916 G A rs762198241 Uncertain_significance DPYD:1806|LOC129930998:129930998 SO:0001583|missense_variant single_nucleotide_variant 2397787
588
+ 1 97920919 C A rs1232582100 Uncertain_significance DPYD:1806|LOC129930998:129930998 SO:0001583|missense_variant single_nucleotide_variant 878991
589
+ 1 97920919 C T Uncertain_significance DPYD:1806|LOC129930998:129930998 SO:0001583|missense_variant single_nucleotide_variant 4071713
590
+ 1 97920920 C T rs768020954 Likely_pathogenic DPYD:1806|LOC129930998:129930998 SO:0001582|initiator_codon_variant;SO:0001583|missense_variant single_nucleotide_variant 370476
591
+ 1 97920922 T G rs772950053 Likely_pathogenic DPYD:1806|LOC129930998:129930998 SO:0001582|initiator_codon_variant;SO:0001583|missense_variant single_nucleotide_variant 2506136
592
+ 1 97921030 A G rs886046581 Uncertain_significance DPYD:1806|LOC129930998:129930998 SO:0001623|5_prime_UTR_variant single_nucleotide_variant 298302
593
+ 1 97921034 T C rs868725176 Uncertain_significance DPYD:1806|LOC129930998:129930998 SO:0001623|5_prime_UTR_variant single_nucleotide_variant 298303
594
+ 1 97921044 G T rs886046582 Uncertain_significance DPYD:1806|LOC129930998:129930998 SO:0001623|5_prime_UTR_variant single_nucleotide_variant 298304
595
+ 1 97921066 G A rs554389296 Uncertain_significance DPYD:1806|LOC129930998:129930998 single_nucleotide_variant 880212
596
+ 1 97921165 C T rs72981743 Benign DPYD:1806|LOC129930998:129930998 single_nucleotide_variant 1266319
597
+ 1 97921399 A C rs61787828 Benign DPYD:1806 single_nucleotide_variant 1243886
data/cpic_dpyd_function.csv ADDED
@@ -0,0 +1,14 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ allele,rsid,alt,cpic_function,label_class,source
2
+ *2A,rs3918290,T,No function,no_function,CPIC v2024.01 (anukriti-pgx-core pinned)
3
+ *4,rs1801158,T,Normal function,normal_function,CPIC v2024.01 (anukriti-pgx-core pinned)
4
+ *5,rs1801159,A,Normal function,normal_function,CPIC v2024.01 (anukriti-pgx-core pinned)
5
+ *6,rs1801160,A,Decreased function,decreased_function,CPIC v2024.01 (anukriti-pgx-core pinned)
6
+ *9A,rs1801265,C,Normal function,normal_function,CPIC v2024.01 (anukriti-pgx-core pinned)
7
+ *10,rs1801266,A,Decreased function,decreased_function,CPIC v2024.01 (anukriti-pgx-core pinned)
8
+ *12,rs78060119,C,No function,no_function,CPIC v2024.01 (anukriti-pgx-core pinned)
9
+ *13,rs55886062,A,No function,no_function,CPIC v2024.01 (anukriti-pgx-core pinned)
10
+ c.1679T>G,rs55971861,G,No function,no_function,CPIC v2024.01 (anukriti-pgx-core pinned)
11
+ c.2846A>T,rs67376798,T,Decreased function,decreased_function,CPIC v2024.01 (anukriti-pgx-core pinned)
12
+ HapB3,rs56038477,C,Decreased function,decreased_function,CPIC v2024.01 (anukriti-pgx-core pinned)
13
+ c.1236G>A,rs56293913,A,Uncertain function,unknown,CPIC v2024.01 (anukriti-pgx-core pinned)
14
+ M166V,rs2297595,C,Normal function,normal_function,CPIC v2024.01 (anukriti-pgx-core pinned)
data/gnomad_dpyd_sas.csv ADDED
@@ -0,0 +1,121 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ variant_id,rsid,chrom,pos,ref,alt,gnomad_global_af,gnomad_sas_af,in_gnomad,source_dataset
2
+ 1-97078992-A-G,rs770320798,1,97078992,A,G,3.942699434879748e-05,0.0,1,gnomad_r4
3
+ 1-97078993-C-G,rs148799944,1,97078993,C,G,7.231133315803314e-05,0.0,1,gnomad_r4
4
+ 1-97079002-G-C,rs956842768,1,97079002,G,C,2.629433882885015e-05,0.0,1,gnomad_r4
5
+ 1-97079005-C-T,rs140114515,1,97079005,C,T,3.2878297693258634e-05,0.0,1,gnomad_r4
6
+ 1-97079012-CTT-C,rs1557849648,1,97079012,CTT,C,6.573757559821194e-06,0.0,1,gnomad_r4
7
+ 1-97079020-C-A,rs761584058,1,97079020,C,A,6.574362615544423e-06,0.0,1,gnomad_r4
8
+ 1-97079022-T-TA,rs1459699844,1,97079022,T,TA,1.3146996568633896e-05,0.0,1,gnomad_r4
9
+ 1-97079056-C-T,rs151074666,1,97079056,C,T,0.00017112468407750632,0.0,1,gnomad_r4
10
+ 1-97079060-A-G,rs1465795668,1,97079060,A,G,,,0,gnomad_r4
11
+ 1-97079062-T-C,rs745982505,1,97079062,T,C,1.9731909127981164e-05,0.0,1,gnomad_r4
12
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+ 1,97082389,C,T,rs763862486,1-97082389-C-T,3.944358252912251e-05,0.0,-4.402923987471806,-7.0,1,0,missense_variant,uncertain_significance,0,,,
29
+ 1,97082397,A,G,rs2101558314,1-97082397-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
30
+ 1,97082415,A,G,rs748639205,1-97082415-A-G,2.737082680425069e-06,2.3190019015815594e-05,-5.547128007479037,-4.632830156872773,1,1,missense_variant,uncertain_significance,0,,,
31
+ 1,97082430,C,T,rs1649223892,1-97082430-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
32
+ 1,97082460,C,T,,1-97082460-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
33
+ 1,97082472,T,A,,1-97082472-T-A,,,-7.0,-7.0,0,0,splice_acceptor_variant,,0,,,
34
+ 1,97098485,T,A,,1-97098485-T-A,,,-7.0,-7.0,0,0,intron_variant,,0,,,
35
+ 1,97098497,T,G,rs886046575,1-97098497-T-G,6.573411863693732e-06,0.0,-5.175652070921791,-7.0,1,0,missense_variant,uncertain_significance,0,,,
36
+ 1,97098502,A,G,,1-97098502-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
37
+ 1,97098577,T,C,,1-97098577-T-C,,,-7.0,-7.0,0,0,missense_variant,conflicting_classifications_of_pathogenicity,0,,,
38
+ 1,97098598,C,T,rs1801267,1-97098598-C-T,3.2875703540055755e-05,0.0002072109407376,-4.48180592996493,-3.683377777613875,1,1,missense_variant,uncertain_significance,0,,,
39
+ 1,97098601,T,C,rs2524094303,1-97098601-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
40
+ 1,97098616,C,A,,1-97098616-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
41
+ 1,97098621,A,C,rs919596571,1-97098621-A-C,6.574967782657865e-06,0.0,-5.175550826120342,-7.0,1,0,missense_variant,uncertain_significance,0,,,
42
+ 1,97098623,T,C,rs762911226,1-97098623-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
43
+ 1,97098632,T,G,,1-97098632-T-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
44
+ 1,97192771,C,A,,1-97192771-C-A,,,-7.0,-7.0,0,0,intron_variant,,0,,,
45
+ 1,97193067,A,C,,1-97193067-A-C,,,-7.0,-7.0,0,0,splice_donor_variant,,0,,,
46
+ 1,97193067,A,G,,1-97193067-A-G,,,-7.0,-7.0,0,0,splice_donor_variant,,0,,,
47
+ 1,97193072,G,C,,1-97193072-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
48
+ 1,97193091,C,T,,1-97193091-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
49
+ 1,97193092,G,A,rs557220418,1-97193092-G-A,2.626947224630257e-05,0.0,-4.578898562008317,-7.0,1,0,missense_variant,uncertain_significance,0,,,
50
+ 1,97193093,T,C,rs672601274,1-97193093-T-C,,,-7.0,-7.0,0,0,synonymous_variant,not_provided,0,,,
51
+ 1,97193098,C,A,rs773815814,1-97193098-C-A,4.788905064745996e-06,0.0,-5.310788396006211,-7.0,1,0,missense_variant,uncertain_significance,0,,,
52
+ 1,97193106,C,A,,1-97193106-C-A,,,-7.0,-7.0,0,0,missense_variant,,0,,,
53
+ 1,97193124,G,A,rs752228747,1-97193124-G-A,5.909932626768055e-05,0.0008285004142502,-4.227683235842851,-3.08165485391664,1,1,missense_variant,uncertain_significance,0,,,
54
+ 1,97193127,G,C,rs1031125025,1-97193127-G-C,1.971453355413611e-05,0.0,-4.703016146758968,-7.0,1,0,missense_variant,uncertain_significance,0,,,
55
+ 1,97193142,T,C,,1-97193142-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
56
+ 1,97193143,C,T,,1-97193143-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
57
+ 1,97193159,T,C,rs672601275,1-97193159-T-C,,,-7.0,-7.0,0,0,synonymous_variant,not_provided,0,,,
58
+ 1,97193163,A,G,rs571114616,1-97193163-A-G,6.570388572780194e-06,0.0,-5.1758488662185504,-7.0,1,0,missense_variant,uncertain_significance,0,,,
59
+ 1,97193166,C,A,rs886046576,1-97193166-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
60
+ 1,97193197,T,C,rs1218404593,1-97193197-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
61
+ 1,97193206,C,T,rs199777072,1-97193206-C-T,,,-7.0,-7.0,0,0,missense_variant,conflicting_classifications_of_pathogenicity,0,,,
62
+ 1,97193317,T,C,,1-97193317-T-C,,,-7.0,-7.0,0,0,intron_variant,,0,,,
63
+ 1,97234847,A,G,,1-97234847-A-G,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
64
+ 1,97234871,C,T,,1-97234871-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
65
+ 1,97234878,G,T,rs1241910237,1-97234878-G-T,6.57323902926406e-06,0.0,-5.17566331884304,-7.0,1,0,missense_variant,uncertain_significance,0,,,
66
+ 1,97234902,A,C,,1-97234902-A-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
67
+ 1,97234916,G,A,rs547099198,1-97234916-G-A,3.286403491475069e-05,0.0,-4.4819596345368025,-7.0,1,0,missense_variant,uncertain_significance,0,,,
68
+ 1,97234937,G,T,rs777673186,1-97234937-G-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
69
+ 1,97234946,C,A,,1-97234946-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
70
+ 1,97234947,G,A,rs770958862,1-97234947-G-A,1.9154283650313923e-05,3.478180216110931e-05,-4.715472634532968,-4.457401085425057,1,1,missense_variant,uncertain_significance,0,,,
71
+ 1,97234959,T,C,rs1365638731,1-97234959-T-C,6.584232081012392e-06,0.0,-5.174948479521728,-7.0,1,0,missense_variant,uncertain_significance,0,,,
72
+ 1,97234965,C,A,rs672601276,1-97234965-C-A,,,-7.0,-7.0,0,0,missense_variant,not_provided,0,,,
73
+ 1,97234974,C,T,rs1304906107,1-97234974-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
74
+ 1,97234980,G,T,rs2524775725,1-97234980-G-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
75
+ 1,97234986,T,C,,1-97234986-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
76
+ 1,97234991,G,T,rs56005131,1-97234991-G-T,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,,,
77
+ 1,97234993,C,A,rs672601277,1-97234993-C-A,,,-7.0,-7.0,0,0,synonymous_variant,not_provided,0,,,
78
+ 1,97235034,C,A,rs672601278,1-97235034-C-A,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
79
+ 1,97235103,A,G,rs672601279,1-97235103-A-G,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
80
+ 1,97305159,G,A,rs34534958,1-97305159-G-A,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
81
+ 1,97305277,T,C,,1-97305277-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
82
+ 1,97305279,G,A,rs112766203,1-97305279-G-A,,,-7.0,-7.0,0,0,missense_variant,conflicting_classifications_of_pathogenicity,0,,,
83
+ 1,97305282,C,T,rs267598786,1-97305282-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
84
+ 1,97305289,C,G,rs2101035792,1-97305289-C-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
85
+ 1,97305291,A,G,,1-97305291-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
86
+ 1,97305316,C,T,,1-97305316-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
87
+ 1,97305363,A,C,,1-97305363-A-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
88
+ 1,97305365,G,A,rs139543981,1-97305365-G-A,,,-7.0,-7.0,0,0,synonymous_variant,uncertain_significance,0,,,
89
+ 1,97305372,G,A,rs146529561,1-97305372-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
90
+ 1,97305375,C,A,rs2101036846,1-97305375-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
91
+ 1,97305376,C,T,,1-97305376-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
92
+ 1,97305389,C,T,rs377136032,1-97305389-C-T,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
93
+ 1,97305422,A,G,rs672601280,1-97305422-A-G,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
94
+ 1,97305449,C,G,,1-97305449-C-G,,,-7.0,-7.0,0,0,intron_variant,,0,,,
95
+ 1,97306171,T,A,,1-97306171-T-A,,,-7.0,-7.0,0,0,intron_variant,,0,,,
96
+ 1,97306176,C,CCTT,,1-97306176-C-CCTT,,,-7.0,-7.0,0,0,other,uncertain_significance,1,,,
97
+ 1,97306177,C,A,,1-97306177-C-A,,,-7.0,-7.0,0,0,missense_variant,,0,,,
98
+ 1,97306188,G,C,rs1553251908,1-97306188-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
99
+ 1,97306195,C,T,rs145548112,1-97306195-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
100
+ 1,97306208,A,T,rs1399492718,1-97306208-A-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
101
+ 1,97306240,A,T,,1-97306240-A-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
102
+ 1,97306246,T,A,,1-97306246-T-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
103
+ 1,97306269,C,T,,1-97306269-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
104
+ 1,97306272,C,A,rs1336020354,1-97306272-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
105
+ 1,97306276,T,C,rs756890859,1-97306276-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
106
+ 1,97306281,C,A,rs375436137,1-97306281-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
107
+ 1,97306281,C,T,rs375436137,1-97306281-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
108
+ 1,97306282,G,A,rs538703919,1-97306282-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
109
+ 1,97306285,C,A,rs202212118,1-97306285-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
110
+ 1,97306288,G,C,,1-97306288-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
111
+ 1,97306519,A,G,,1-97306519-A-G,,,-7.0,-7.0,0,0,intron_variant,,0,,,
112
+ 1,97373519,T,C,rs368002831,1-97373519-T-C,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
113
+ 1,97373570,G,C,rs183475941,1-97373570-G-C,,,-7.0,-7.0,0,0,synonymous_variant,conflicting_classifications_of_pathogenicity,0,,,
114
+ 1,97373572,C,T,rs2525630867,1-97373572-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
115
+ 1,97373592,C,G,,1-97373592-C-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
116
+ 1,97373596,T,C,rs763506271,1-97373596-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
117
+ 1,97373629,C,A,rs138545885,1-97373629-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
118
+ 1,97373635,C,T,rs1671426656,1-97373635-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
119
+ 1,97373644,C,G,,1-97373644-C-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
120
+ 1,97373645,C,A,,1-97373645-C-A,,,-7.0,-7.0,0,0,splice_acceptor_variant,,0,,,
121
+ 1,97382392,C,T,rs772254904,1-97382392-C-T,,,-7.0,-7.0,0,0,splice_donor_variant,conflicting_classifications_of_pathogenicity,0,,,
122
+ 1,97382428,T,C,,1-97382428-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
123
+ 1,97382430,T,C,rs780120302,1-97382430-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
124
+ 1,97382442,A,G,rs2101564724,1-97382442-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
125
+ 1,97382452,C,A,rs2525684263,1-97382452-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
126
+ 1,97382460,A,G,rs1346856479,1-97382460-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
127
+ 1,97450042,T,C,rs369990607,1-97450042-T-C,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
128
+ 1,97450053,A,T,,1-97450053-A-T,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
129
+ 1,97450054,C,T,,1-97450054-C-T,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
130
+ 1,97450058,C,A,,1-97450058-C-A,,,-7.0,-7.0,0,0,splice_donor_variant,,0,,,
131
+ 1,97450059,G,A,rs3918289,1-97450059-G-A,,,-7.0,-7.0,0,0,synonymous_variant,conflicting_classifications_of_pathogenicity,0,,,
132
+ 1,97450065,TG,T,rs72549303,1-97450065-TG-T,,,-7.0,-7.0,0,0,frameshift_variant,drug_response,1,,,
133
+ 1,97450068,A,G,rs17376848,1-97450068-A-G,,,-7.0,-7.0,0,0,synonymous_variant,drug_response,0,,,
134
+ 1,97450099,C,T,,1-97450099-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
135
+ 1,97450114,G,A,,1-97450114-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
136
+ 1,97450144,A,G,rs1676330398,1-97450144-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
137
+ 1,97450168,A,G,rs147601618,1-97450168-A-G,,,-7.0,-7.0,0,0,missense_variant,conflicting_classifications_of_pathogenicity,0,,,
138
+ 1,97450189,C,T,rs138616379,1-97450189-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
139
+ 1,97450190,G,A,rs59086055,1-97450190-G-A,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,,,
140
+ 1,97450207,A,G,rs374527058,1-97450207-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
141
+ 1,97450220,T,C,rs889910324,1-97450220-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
142
+ 1,97450233,G,C,,1-97450233-G-C,,,-7.0,-7.0,0,0,intron_variant,,0,,,
143
+ 1,97450288,G,A,rs672601281,1-97450288-G-A,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
144
+ 1,97515733,A,G,rs778754188,1-97515733-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
145
+ 1,97515737,A,C,rs2524204644,1-97515737-A-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
146
+ 1,97515738,G,C,rs886553467,1-97515738-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
147
+ 1,97515748,G,T,,1-97515748-G-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
148
+ 1,97515749,T,G,,1-97515749-T-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
149
+ 1,97515766,C,T,rs1188134745,1-97515766-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
150
+ 1,97515791,T,C,,1-97515791-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
151
+ 1,97515796,G,A,rs754125729,1-97515796-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
152
+ 1,97515812,T,C,rs771648776,1-97515812-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
153
+ 1,97515815,C,A,,1-97515815-C-A,,,-7.0,-7.0,0,0,missense_variant,,0,,,
154
+ 1,97515815,C,T,rs777425216,1-97515815-C-T,,,-7.0,-7.0,0,0,missense_variant,conflicting_classifications_of_pathogenicity,0,,,
155
+ 1,97515851,C,T,rs142619737,1-97515851-C-T,,,-7.0,-7.0,0,0,missense_variant,conflicting_classifications_of_pathogenicity,0,,,
156
+ 1,97515852,G,A,rs760853559,1-97515852-G-A,,,-7.0,-7.0,0,0,synonymous_variant,uncertain_significance,0,,,
157
+ 1,97515857,T,G,,1-97515857-T-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
158
+ 1,97515886,G,A,rs886046577,1-97515886-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
159
+ 1,97515901,G,A,,1-97515901-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
160
+ 1,97515904,A,G,,1-97515904-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
161
+ 1,97515911,G,A,rs672601282,1-97515911-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
162
+ 1,97515913,T,C,,1-97515913-T-C,,,-7.0,-7.0,0,0,missense_variant,,0,,,
163
+ 1,97515923,C,T,rs148994843,1-97515923-C-T,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,,,
164
+ 1,97515928,G,A,rs760663364,1-97515928-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
165
+ 1,97515928,G,C,rs760663364,1-97515928-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
166
+ 1,97515929,C,G,rs1648195326,1-97515929-C-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
167
+ 1,97515950,T,C,rs56056384,1-97515950-T-C,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
168
+ 1,97515958,A,T,,1-97515958-A-T,,,-7.0,-7.0,0,0,intron_variant,,0,,,
169
+ 1,97516150,C,A,,1-97516150-C-A,,,-7.0,-7.0,0,0,intron_variant,,0,,,
170
+ 1,97549360,G,A,,1-97549360-G-A,,,-7.0,-7.0,0,0,intron_variant,,0,,,
171
+ 1,97549485,T,C,,1-97549485-T-C,,,-7.0,-7.0,0,0,intron_variant,,0,,,
172
+ 1,97549554,G,C,,1-97549554-G-C,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
173
+ 1,97549560,C,T,rs775930761,1-97549560-C-T,,,-7.0,-7.0,0,0,synonymous_variant,uncertain_significance,0,,,
174
+ 1,97549564,A,G,rs2524372985,1-97549564-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
175
+ 1,97549590,T,A,,1-97549590-T-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
176
+ 1,97549612,T,A,rs1264198400,1-97549612-T-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
177
+ 1,97549669,C,T,rs776082092,1-97549669-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
178
+ 1,97549679,T,A,rs2524373962,1-97549679-T-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
179
+ 1,97549687,G,A,,1-97549687-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
180
+ 1,97549694,C,T,rs912917991,1-97549694-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
181
+ 1,97549715,T,C,rs750147471,1-97549715-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
182
+ 1,97549726,G,C,rs144395748,1-97549726-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
183
+ 1,97549729,C,T,rs1557791062,1-97549729-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
184
+ 1,97549735,G,A,rs72975710,1-97549735-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
185
+ 1,97549735,G,C,rs72975710,1-97549735-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
186
+ 1,97549740,T,C,,1-97549740-T-C,,,-7.0,-7.0,0,0,synonymous_variant,,0,,,
187
+ 1,97549747,G,C,rs193920862,1-97549747-G-C,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
188
+ 1,97549758,T,G,rs886046578,1-97549758-T-G,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
189
+ 1,97549863,T,C,,1-97549863-T-C,,,-7.0,-7.0,0,0,intron_variant,,0,,,
190
+ 1,97573760,C,A,,1-97573760-C-A,,,-7.0,-7.0,0,0,missense_variant,,0,,,
191
+ 1,97573762,T,G,rs200709381,1-97573762-T-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
192
+ 1,97573765,G,C,,1-97573765-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
193
+ 1,97573789,G,A,rs1290815802,1-97573789-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
194
+ 1,97573804,T,C,,1-97573804-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
195
+ 1,97573826,G,C,rs1165667490,1-97573826-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
196
+ 1,97573834,T,C,rs757155354,1-97573834-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
197
+ 1,97573858,T,A,,1-97573858-T-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
198
+ 1,97573862,G,A,,1-97573862-G-A,,,-7.0,-7.0,0,0,other,,0,,,
199
+ 1,97573870,C,T,rs199646142,1-97573870-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
200
+ 1,97573871,G,A,rs528430685,1-97573871-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
201
+ 1,97573879,T,C,rs886046579,1-97573879-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
202
+ 1,97573881,C,T,rs61622928,1-97573881-C-T,,,-7.0,-7.0,0,0,missense_variant,conflicting_classifications_of_pathogenicity,0,,,
203
+ 1,97573886,C,A,,1-97573886-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
204
+ 1,97573919,G,A,rs140602333,1-97573919-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
205
+ 1,97573951,T,A,,1-97573951-T-A,,,-7.0,-7.0,0,0,missense_variant,,0,,,
206
+ 1,97573960,G,C,rs1354585423,1-97573960-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
207
+ 1,97573970,T,C,rs144935781,1-97573970-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
208
+ 1,97573981,A,C,rs672601283,1-97573981-A-C,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
209
+ 1,97573985,A,G,rs56293913,1-97573985-A-G,,,-7.0,-7.0,0,0,intron_variant,benign,0,unknown,CPIC,Uncertain function
210
+ 1,97579893,G,C,rs75017182,1-97579893-G-C,,,-7.0,-7.0,0,0,intron_variant,drug_response,0,,,
211
+ 1,97592953,A,C,,1-97592953-A-C,,,-7.0,-7.0,0,0,intron_variant,,0,,,
212
+ 1,97593229,C,T,,1-97593229-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
213
+ 1,97593238,T,C,rs72549305,1-97593238-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
214
+ 1,97593276,C,T,rs377143350,1-97593276-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
215
+ 1,97593292,G,C,,1-97593292-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
216
+ 1,97593298,A,G,rs771885007,1-97593298-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
217
+ 1,97593315,G,A,,1-97593315-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
218
+ 1,97593319,T,A,rs886046580,1-97593319-T-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
219
+ 1,97593322,C,T,rs183385770,1-97593322-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
220
+ 1,97593343,C,A,rs72549306,1-97593343-C-A,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,,,
221
+ 1,97593351,C,T,rs747633945,1-97593351-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
222
+ 1,97593352,G,A,rs757994597,1-97593352-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
223
+ 1,97593353,T,C,rs1260688429,1-97593353-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
224
+ 1,97593357,G,T,,1-97593357-G-T,,,-7.0,-7.0,0,0,other,,0,,,
225
+ 1,97593370,A,G,rs770566506,1-97593370-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
226
+ 1,97593379,C,T,rs201018345,1-97593379-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
227
+ 1,97593438,A,C,,1-97593438-A-C,,,-7.0,-7.0,0,0,intron_variant,,0,,,
228
+ 1,97593438,A,G,rs115349832,1-97593438-A-G,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
229
+ 1,97595023,T,C,rs114968502,1-97595023-T-C,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
230
+ 1,97595124,G,A,,1-97595124-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
231
+ 1,97595130,C,T,rs672601284,1-97595130-C-T,,,-7.0,-7.0,0,0,missense_variant,not_provided,0,,,
232
+ 1,97595140,T,C,rs779925747,1-97595140-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
233
+ 1,97595145,T,C,,1-97595145-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
234
+ 1,97595148,T,C,rs672601285,1-97595148-T-C,,,-7.0,-7.0,0,0,missense_variant,not_provided,0,,,
235
+ 1,97595149,T,C,rs146356975,1-97595149-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
236
+ 1,97595166,C,A,,1-97595166-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
237
+ 1,97679005,A,G,rs672601286,1-97679005-A-G,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
238
+ 1,97679082,G,A,rs1660302424,1-97679082-G-A,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
239
+ 1,97679094,C,A,,1-97679094-C-A,,,-7.0,-7.0,0,0,splice_donor_variant,,0,,,
240
+ 1,97679104,T,C,rs746329786,1-97679104-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
241
+ 1,97679120,G,A,,1-97679120-G-A,,,-7.0,-7.0,0,0,synonymous_variant,,0,,,
242
+ 1,97679155,T,C,,1-97679155-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
243
+ 1,97679170,T,C,rs45589337,1-97679170-T-C,,,-7.0,-7.0,0,0,missense_variant,conflicting_classifications_of_pathogenicity,0,,,
244
+ 1,97679173,C,T,rs141726921,1-97679173-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
245
+ 1,97679175,C,T,rs764945792,1-97679175-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
246
+ 1,97679177,A,C,rs556933127,1-97679177-A-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
247
+ 1,97679199,T,C,,1-97679199-T-C,,,-7.0,-7.0,0,0,intron_variant,,0,,,
248
+ 1,97691712,T,A,rs1033092437,1-97691712-T-A,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
249
+ 1,97691717,C,A,,1-97691717-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
250
+ 1,97691736,A,G,rs2524346611,1-97691736-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
251
+ 1,97691740,G,A,rs376128878,1-97691740-G-A,,,-7.0,-7.0,0,0,synonymous_variant,uncertain_significance,0,,,
252
+ 1,97691742,T,G,,1-97691742-T-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
253
+ 1,97691748,T,G,rs1185250556,1-97691748-T-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
254
+ 1,97691753,A,T,,1-97691753-A-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
255
+ 1,97691769,G,A,rs780025995,1-97691769-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
256
+ 1,97691785,G,T,,1-97691785-G-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
257
+ 1,97699345,C,G,,1-97699345-C-G,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
258
+ 1,97699351,C,T,,1-97699351-C-T,,,-7.0,-7.0,0,0,missense_variant,,0,,,
259
+ 1,97699392,G,A,rs190048823,1-97699392-G-A,,,-7.0,-7.0,0,0,synonymous_variant,uncertain_significance,0,,,
260
+ 1,97699399,T,C,rs72549307,1-97699399-T-C,,,-7.0,-7.0,0,0,missense_variant,conflicting_classifications_of_pathogenicity,0,,,
261
+ 1,97699403,C,A,,1-97699403-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
262
+ 1,97699408,C,A,rs376073289,1-97699408-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
263
+ 1,97699408,C,T,rs376073289,1-97699408-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
264
+ 1,97699474,T,C,rs115232898,1-97699474-T-C,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,,,
265
+ 1,97699475,A,C,,1-97699475-A-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
266
+ 1,97699483,G,C,,1-97699483-G-C,,,-7.0,-7.0,0,0,missense_variant,,0,,,
267
+ 1,97699486,A,T,rs779728902,1-97699486-A-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
268
+ 1,97699489,T,G,rs672601287,1-97699489-T-G,,,-7.0,-7.0,0,0,missense_variant,not_provided,0,,,
269
+ 1,97699511,G,T,,1-97699511-G-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
270
+ 1,97699520,T,A,,1-97699520-T-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
271
+ 1,97699534,A,G,rs763061658,1-97699534-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
272
+ 1,97699542,G,C,,1-97699542-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
273
+ 1,97699551,C,T,rs202011255,1-97699551-C-T,,,-7.0,-7.0,0,0,intron_variant,conflicting_classifications_of_pathogenicity,0,,,
274
+ 1,97699552,G,A,rs767955683,1-97699552-G-A,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
275
+ 1,97720901,A,G,rs2524533594,1-97720901-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
276
+ 1,97721505,C,T,rs373218392,1-97721505-C-T,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
277
+ 1,97721518,C,A,,1-97721518-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
278
+ 1,97721542,T,C,rs200562975,1-97721542-T-C,,,-7.0,-7.0,0,0,missense_variant,conflicting_classifications_of_pathogenicity,0,,,
279
+ 1,97721545,T,C,,1-97721545-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
280
+ 1,97721571,T,C,,1-97721571-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
281
+ 1,97721577,C,T,,1-97721577-C-T,,,-7.0,-7.0,0,0,missense_variant,,0,,,
282
+ 1,97721626,C,T,rs778022685,1-97721626-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
283
+ 1,97721648,C,G,rs377169736,1-97721648-C-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
284
+ 1,97721653,T,C,rs2524539694,1-97721653-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
285
+ 1,97721665,A,G,rs1283205838,1-97721665-A-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
286
+ 1,97740377,T,G,rs370363977,1-97740377-T-G,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
287
+ 1,97740391,C,T,rs746368304,1-97740391-C-T,,,-7.0,-7.0,0,0,splice_donor_variant,conflicting_classifications_of_pathogenicity,0,,,
288
+ 1,97740439,G,C,rs143986398,1-97740439-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
289
+ 1,97740441,C,A,rs928681171,1-97740441-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
290
+ 1,97740444,C,A,rs672601288,1-97740444-C-A,,,-7.0,-7.0,0,0,missense_variant,not_provided,0,,,
291
+ 1,97740448,T,A,rs672601289,1-97740448-T-A,,,-7.0,-7.0,0,0,other,not_provided,0,,,
292
+ 1,97740450,T,C,,1-97740450-T-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
293
+ 1,97740501,T,C,,1-97740501-T-C,,,-7.0,-7.0,0,0,intron_variant,,0,,,
294
+ 1,97740560,C,T,rs552156826,1-97740560-C-T,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
295
+ 1,97828078,A,G,rs672601290,1-97828078-A-G,,,-7.0,-7.0,0,0,intron_variant,not_provided,0,,,
296
+ 1,97828116,C,T,,1-97828116-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
297
+ 1,97828127,G,A,rs189768576,1-97828127-G-A,,,-7.0,-7.0,0,0,other,conflicting_classifications_of_pathogenicity,0,,,
298
+ 1,97828129,A,C,rs762102298,1-97828129-A-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
299
+ 1,97828138,C,T,rs767818267,1-97828138-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
300
+ 1,97828153,G,A,rs371587702,1-97828153-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
301
+ 1,97828158,C,G,rs2101479863,1-97828158-C-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
302
+ 1,97828159,T,G,rs2101479885,1-97828159-T-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
303
+ 1,97828160,T,C,rs367619008,1-97828160-T-C,,,-7.0,-7.0,0,0,missense_variant,conflicting_classifications_of_pathogenicity,0,,,
304
+ 1,97828162,A,T,rs2525245478,1-97828162-A-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
305
+ 1,97828166,C,G,rs1557992438,1-97828166-C-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
306
+ 1,97828169,C,A,,1-97828169-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
307
+ 1,97828196,T,G,,1-97828196-T-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
308
+ 1,97828249,T,A,,1-97828249-T-A,,,-7.0,-7.0,0,0,intron_variant,,0,,,
309
+ 1,97883268,C,A,,1-97883268-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
310
+ 1,97883273,C,A,,1-97883273-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
311
+ 1,97883277,T,G,rs756684474,1-97883277-T-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
312
+ 1,97883328,C,T,rs528768620,1-97883328-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
313
+ 1,97883341,G,A,rs775601164,1-97883341-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
314
+ 1,97883366,C,T,rs763165014,1-97883366-C-T,,,-7.0,-7.0,0,0,synonymous_variant,conflicting_classifications_of_pathogenicity,0,,,
315
+ 1,97920880,G,C,rs1439572087,1-97920880-G-C,,,-7.0,-7.0,0,0,intron_variant,uncertain_significance,0,,,
316
+ 1,97920886,C,T,rs769820114,1-97920886-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
317
+ 1,97920887,G,C,rs376273539,1-97920887-G-C,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
318
+ 1,97920916,G,A,rs762198241,1-97920916-G-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
319
+ 1,97920919,C,A,rs1232582100,1-97920919-C-A,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
320
+ 1,97920919,C,T,,1-97920919-C-T,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,,,
321
+ 1,97921030,A,G,rs886046581,1-97921030-A-G,,,-7.0,-7.0,0,0,other,uncertain_significance,0,,,
322
+ 1,97921034,T,C,rs868725176,1-97921034-T-C,,,-7.0,-7.0,0,0,other,uncertain_significance,0,,,
323
+ 1,97921044,G,T,rs886046582,1-97921044-G-T,,,-7.0,-7.0,0,0,other,uncertain_significance,0,,,
324
+ 1,97921066,G,A,rs554389296,1-97921066-G-A,,,-7.0,-7.0,0,0,other,uncertain_significance,0,,,
data/training_data.csv ADDED
@@ -0,0 +1,274 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,pos,ref,alt,rsid,variant_id,gnomad_global_af,gnomad_sas_af,log10_gnomad_global_af,log10_gnomad_sas_af,in_gnomad,sas_enriched,consequence,clnsig_norm,is_indel,label_class,label_source,cpic_function
2
+ 1,97079060,A,G,rs1465795668,1-97079060-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
3
+ 1,97079078,A,G,rs2524010261,1-97079078-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
4
+ 1,97079133,T,A,rs72547602,1-97079133-T-A,,,-7.0,-7.0,0,0,missense_variant,pathogenic,0,no_function,ClinVar,
5
+ 1,97079204,C,G,rs17116357,1-97079204-C-G,0.1427697690324617,0.1016209476309226,-0.8453634388741365,-0.9930163321773123,1,0,intron_variant,benign,0,normal_function,ClinVar,
6
+ 1,97079215,T,C,rs290855,1-97079215-T-C,0.8023119714883152,0.8923683119037744,-0.09565667340722225,-0.049455811291255036,1,1,intron_variant,benign,0,normal_function,ClinVar,
7
+ 1,97079354,T,C,rs76665493,1-97079354-T-C,0.0040596999237985,0.0002075550020755,-2.3914953689182132,-3.682657602971522,1,0,intron_variant,likely_benign,0,normal_function,ClinVar,
8
+ 1,97082275,G,A,rs290854,1-97082275-G-A,0.9999737267317368,1.0,-1.1367054737244114e-05,4.3429446044209946e-08,1,1,intron_variant,benign,0,normal_function,ClinVar,
9
+ 1,97082329,C,G,rs2101557799,1-97082329-C-G,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
10
+ 1,97082391,T,A,rs67376798,1-97082391-T-A,0.0032778055124937,0.000621632822213,-2.4844035693726045,-3.20639620496621,1,0,missense_variant,drug_response,0,decreased_function,CPIC,Decreased function
11
+ 1,97082394,A,G,rs372307932,1-97082394-A-G,4.789835694950418e-06,0.0,-5.310705733509347,-7.0,1,0,missense_variant,likely_pathogenic,0,no_function,ClinVar,
12
+ 1,97082400,GC,G,rs2524026293,1-97082400-GC-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
13
+ 1,97082404,C,CA,rs2524026345,1-97082404-C-CA,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
14
+ 1,97082435,T,A,,1-97082435-T-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
15
+ 1,97082449,G,A,rs2101558812,1-97082449-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
16
+ 1,97082471,C,T,rs377221676,1-97082471-C-T,6.575140708011152e-06,0.0,-5.175539575196536,-7.0,1,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
17
+ 1,97082803,C,T,rs2171826,1-97082803-C-T,0.1430262379167488,0.1014943960149439,-0.8445839810057932,-0.9935575086389534,1,0,intron_variant,benign,0,normal_function,ClinVar,
18
+ 1,97098470,T,C,rs375268978,1-97098470-T-C,0.0004924491135915,0.0,-3.307550458164722,-7.0,1,0,intron_variant,benign,0,normal_function,ClinVar,
19
+ 1,97098488,C,T,rs1355754530,1-97098488-C-T,1.3164996906225726e-05,0.0,-4.877292846971456,-7.0,1,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
20
+ 1,97098500,GA,G,rs1057516894,1-97098500-GA-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
21
+ 1,97098506,GC,G,rs1057517230,1-97098506-GC-G,6.846173331416405e-07,0.0,-6.105342102012473,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
22
+ 1,97098508,CT,C,rs778614771,1-97098508-CT-C,1.3151837969356215e-05,0.0004163197335553,-4.87772388289004,-3.380468698058938,1,1,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
23
+ 1,97098521,AAC,A,rs1650431372,1-97098521-AAC-A,6.845339145482624e-07,0.0,-6.105388277592908,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
24
+ 1,97098533,T,A,rs1553212596,1-97098533-T-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
25
+ 1,97098550,A,G,rs2524093994,1-97098550-A-G,6.844636337626746e-07,0.0,-6.105427184673952,-7.0,1,0,missense_variant,likely_benign,0,normal_function,ClinVar,
26
+ 1,97098575,T,A,rs1057516873,1-97098575-T-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
27
+ 1,97098581,C,A,rs2524094119,1-97098581-C-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
28
+ 1,97098582,T,C,,1-97098582-T-C,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
29
+ 1,97098602,G,A,rs771839581,1-97098602-G-A,1.3155990580310744e-05,0.0,-4.877587813197691,-7.0,1,0,other,likely_pathogenic,0,no_function,ClinVar,
30
+ 1,97098605,C,A,rs2524094344,1-97098605-C-A,,,-7.0,-7.0,0,0,other,pathogenic,0,no_function,ClinVar,
31
+ 1,97098609,A,G,rs773002572,1-97098609-A-G,1.3150281416022304e-05,0.0002076411960132,-4.877774897868476,-3.6824773723761233,1,1,synonymous_variant,likely_benign,0,normal_function,ClinVar,
32
+ 1,97098640,G,A,rs1570451084,1-97098640-G-A,6.847551589453675e-07,0.0,-6.105265820586007,-7.0,1,0,intron_variant,likely_benign,0,normal_function,ClinVar,
33
+ 1,97192839,C,T,rs4950023,1-97192839-C-T,0.648672473225798,0.8157676348547718,-0.18797446425337414,-0.0884334758412319,1,1,intron_variant,benign,0,normal_function,ClinVar,
34
+ 1,97193068,C,T,rs1057517095,1-97193068-C-T,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
35
+ 1,97193101,G,GT,rs1057517327,1-97193101-G-GT,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
36
+ 1,97193105,C,T,rs903875506,1-97193105-C-T,1.231419251734933e-05,0.0,-4.90608152392773,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
37
+ 1,97193111,CT,C,rs746991079,1-97193111-CT-C,5.25520593838271e-05,0.0,-4.278584637554638,-7.0,1,0,frameshift_variant,pathogenic/likely_pathogenic,1,no_function,ClinVar,
38
+ 1,97193137,G,A,rs1057517271,1-97193137-G-A,6.841227425659802e-07,0.0,-6.105615949755963,-7.0,1,0,other,likely_pathogenic,0,no_function,ClinVar,
39
+ 1,97193138,T,C,,1-97193138-T-C,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
40
+ 1,97193141,A,G,rs777542103,1-97193141-A-G,1.314043179458877e-05,0.0,-4.87809785153156,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
41
+ 1,97193142,TC,T,rs2524554561,1-97193142-TC-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
42
+ 1,97193201,G,T,rs1337420489,1-97193201-G-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
43
+ 1,97234569,C,T,rs11808108,1-97234569-C-T,0.0212810704943675,0.0004144218814753,-1.6720044889115306,-3.3824525392918607,1,0,intron_variant,benign,0,normal_function,ClinVar,
44
+ 1,97234689,T,C,rs17432999,1-97234689-T-C,0.0386853165221959,0.0440016604400166,-1.4124527227738768,-1.3565299477390278,1,1,intron_variant,benign,0,normal_function,ClinVar,
45
+ 1,97234773,A,AT,rs544905665,1-97234773-A-AT,0.0085675211841681,0.0012820512820512,-2.0671397440042187,-2.8920607290419746,1,0,intron_variant,likely_benign,1,normal_function,ClinVar,
46
+ 1,97234851,C,A,,1-97234851-C-A,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
47
+ 1,97234851,C,G,rs1252510761,1-97234851-C-G,6.575918984678109e-06,0.0,-5.17548894232244,-7.0,1,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
48
+ 1,97234854,G,A,rs2524774440,1-97234854-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
49
+ 1,97234873,A,G,rs55725052,1-97234873-A-G,4.5955882352941176e-05,0.0,-4.336714892931369,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
50
+ 1,97234954,GGA,G,rs1162905063,1-97234954-GGA-G,6.572547782422378e-06,0.0,-5.175708307526507,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
51
+ 1,97234956,AGGT,GC,rs1057516510,1-97234956-AGGT-GC,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
52
+ 1,97234995,C,G,,1-97234995-C-G,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
53
+ 1,97235033,C,T,rs12137711,1-97235033-C-T,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
54
+ 1,97305252,C,T,rs369672458,1-97305252-C-T,,,-7.0,-7.0,0,0,intron_variant,likely_benign,0,normal_function,ClinVar,
55
+ 1,97305258,C,T,rs2101035489,1-97305258-C-T,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
56
+ 1,97305271,C,CT,rs1057516828,1-97305271-C-CT,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
57
+ 1,97305275,T,C,,1-97305275-T-C,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
58
+ 1,97305275,T,G,rs772853110,1-97305275-T-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
59
+ 1,97305283,G,A,rs759372918,1-97305283-G-A,,,-7.0,-7.0,0,0,other,pathogenic/likely_pathogenic,0,no_function,ClinVar,
60
+ 1,97305335,C,G,rs1397691452,1-97305335-C-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
61
+ 1,97305348,GT,G,rs1558014211,1-97305348-GT-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
62
+ 1,97305351,T,TTGGTG,,1-97305351-T-TTGGTG,,,-7.0,-7.0,0,0,frameshift_variant,pathogenic,1,no_function,ClinVar,
63
+ 1,97305364,C,T,rs1801160,1-97305364-C-T,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,decreased_function,CPIC,Decreased function
64
+ 1,97305381,A,G,rs74104343,1-97305381-A-G,,,-7.0,-7.0,0,0,intron_variant,benign/likely_benign,0,normal_function,ClinVar,
65
+ 1,97306173,T,C,rs746718279,1-97306173-T-C,,,-7.0,-7.0,0,0,intron_variant,likely_benign,0,normal_function,ClinVar,
66
+ 1,97306175,ACCTT,A,rs1553251903,1-97306175-ACCTT-A,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,1,no_function,ClinVar,
67
+ 1,97306176,C,T,,1-97306176-C-T,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
68
+ 1,97306177,CT,C,rs1553251907,1-97306177-CT-C,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
69
+ 1,97306209,TC,T,rs2525218019,1-97306209-TC-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
70
+ 1,97306210,CA,C,rs1165702486,1-97306210-CA-C,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
71
+ 1,97306220,TG,T,rs1064796552,1-97306220-TG-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
72
+ 1,97306241,A,T,rs753891721,1-97306241-A-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
73
+ 1,97306265,C,T,rs753296078,1-97306265-C-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
74
+ 1,97306291,C,A,rs1667161380,1-97306291-C-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
75
+ 1,97306298,C,A,rs2525218826,1-97306298-C-A,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
76
+ 1,97306299,T,C,rs2525218835,1-97306299-T-C,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
77
+ 1,97306391,C,A,rs7556439,1-97306391-C-A,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
78
+ 1,97373297,G,A,rs74105115,1-97373297-G-A,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
79
+ 1,97373298,C,T,rs55652347,1-97373298-C-T,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
80
+ 1,97373331,T,C,rs11582179,1-97373331-T-C,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
81
+ 1,97373404,C,T,rs115139529,1-97373404-C-T,,,-7.0,-7.0,0,0,intron_variant,likely_benign,0,normal_function,ClinVar,
82
+ 1,97373416,A,G,rs1879374,1-97373416-A-G,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
83
+ 1,97373460,A,G,rs1890138,1-97373460-A-G,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
84
+ 1,97373560,C,G,rs769167857,1-97373560-C-G,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
85
+ 1,97373560,CCTGCCCACAGGCCAGG,C,rs773499329,1-97373560-CCTGCCCACAGGCCAGG-C,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
86
+ 1,97373579,C,CA,rs1057517396,1-97373579-C-CA,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
87
+ 1,97373615,AT,A,rs1057517055,1-97373615-AT-A,,,-7.0,-7.0,0,0,frameshift_variant,pathogenic,1,no_function,ClinVar,
88
+ 1,97373635,CTCCAGAA,C,rs1440380546,1-97373635-CTCCAGAA-C,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,1,no_function,ClinVar,
89
+ 1,97373857,C,G,rs6699630,1-97373857-C-G,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
90
+ 1,97382318,T,C,rs72728438,1-97382318-T-C,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
91
+ 1,97382396,AG,A,rs1057516710,1-97382396-AG-A,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
92
+ 1,97382432,G,T,rs1570632355,1-97382432-G-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
93
+ 1,97382461,T,G,rs55971861,1-97382461-T-G,,,-7.0,-7.0,0,0,missense_variant,uncertain_significance,0,no_function,CPIC,No function
94
+ 1,97382485,T,G,rs12078940,1-97382485-T-G,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
95
+ 1,97382584,G,T,rs56279424,1-97382584-G-T,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
96
+ 1,97450056,T,TA,rs760156122,1-97450056-T-TA,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,1,no_function,ClinVar,
97
+ 1,97450058,C,G,rs3918290,1-97450058-C-G,,,-7.0,-7.0,0,0,splice_donor_variant,pathogenic/likely_pathogenic,0,no_function,CPIC,No function
98
+ 1,97450058,C,T,rs3918290,1-97450058-C-T,,,-7.0,-7.0,0,0,splice_donor_variant,drug_response,0,no_function,CPIC,No function
99
+ 1,97450067,GA,G,rs2523871765,1-97450067-GA-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
100
+ 1,97450101,C,T,rs1057516388,1-97450101-C-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
101
+ 1,97450107,T,G,,1-97450107-T-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
102
+ 1,97450133,C,A,rs1057516671,1-97450133-C-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
103
+ 1,97450142,GAA,G,,1-97450142-GAA-G,,,-7.0,-7.0,0,0,frameshift_variant,pathogenic,1,no_function,ClinVar,
104
+ 1,97450183,GT,G,rs2523873242,1-97450183-GT-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
105
+ 1,97450193,T,TGA,,1-97450193-T-TGA,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
106
+ 1,97450199,TG,T,rs1346124437,1-97450199-TG-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
107
+ 1,97515585,A,AT,rs56080540,1-97515585-A-AT,,,-7.0,-7.0,0,0,intron_variant,benign,1,normal_function,ClinVar,
108
+ 1,97515643,T,TA,rs145228578,1-97515643-T-TA,,,-7.0,-7.0,0,0,intron_variant,benign,1,normal_function,ClinVar,
109
+ 1,97515686,T,C,rs2811178,1-97515686-T-C,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
110
+ 1,97515687,G,A,rs2786783,1-97515687-G-A,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
111
+ 1,97515738,GA,G,rs764584080,1-97515738-GA-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
112
+ 1,97515751,A,AG,rs1290522460,1-97515751-A-AG,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
113
+ 1,97515763,C,T,rs2101975422,1-97515763-C-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
114
+ 1,97515765,T,A,rs148372305,1-97515765-T-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
115
+ 1,97515783,T,G,rs1648178154,1-97515783-T-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
116
+ 1,97515785,G,A,rs1057516968,1-97515785-G-A,,,-7.0,-7.0,0,0,other,pathogenic/likely_pathogenic,0,no_function,ClinVar,
117
+ 1,97515787,A,C,rs55886062,1-97515787-A-C,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,no_function,CPIC,No function
118
+ 1,97515794,AT,A,rs1057517018,1-97515794-AT-A,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
119
+ 1,97515795,T,C,rs780421257,1-97515795-T-C,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
120
+ 1,97515816,G,A,rs149101842,1-97515816-G-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
121
+ 1,97515839,T,C,rs1801159,1-97515839-T-C,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,normal_function,CPIC,Normal function
122
+ 1,97515849,T,C,rs762029458,1-97515849-T-C,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
123
+ 1,97515855,CATTTCTACACT,C,rs2524206318,1-97515855-CATTTCTACACT-C,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
124
+ 1,97515864,A,G,rs1257539978,1-97515864-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
125
+ 1,97515865,C,T,rs1801158,1-97515865-C-T,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,normal_function,CPIC,Normal function
126
+ 1,97515891,G,C,rs752329473,1-97515891-G-C,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
127
+ 1,97515892,TAAAAGA,GT,rs2524206768,1-97515892-TAAAAGA-GT,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
128
+ 1,97515912,C,T,rs369465750,1-97515912-C-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
129
+ 1,97515942,C,G,rs766535034,1-97515942-C-G,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
130
+ 1,97515943,T,C,rs2524207205,1-97515943-T-C,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
131
+ 1,97515952,C,T,rs55699321,1-97515952-C-T,,,-7.0,-7.0,0,0,intron_variant,benign/likely_benign,0,normal_function,ClinVar,
132
+ 1,97516031,C,T,rs6657204,1-97516031-C-T,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
133
+ 1,97516066,G,GA,rs141050810,1-97516066-G-GA,,,-7.0,-7.0,0,0,intron_variant,benign,1,normal_function,ClinVar,
134
+ 1,97516150,C,T,rs1337752,1-97516150-C-T,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
135
+ 1,97549384,C,A,rs2786525,1-97549384-C-A,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
136
+ 1,97549544,G,T,rs199469537,1-97549544-G-T,,,-7.0,-7.0,0,0,intron_variant,likely_benign,0,normal_function,ClinVar,
137
+ 1,97549559,C,T,rs1057517126,1-97549559-C-T,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
138
+ 1,97549565,C,T,rs138391898,1-97549565-C-T,,,-7.0,-7.0,0,0,missense_variant,likely_benign,0,normal_function,ClinVar,
139
+ 1,97549565,CG,C,rs1057516615,1-97549565-CG-C,,,-7.0,-7.0,0,0,other,likely_pathogenic,1,no_function,ClinVar,
140
+ 1,97549582,C,T,rs1214305633,1-97549582-C-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
141
+ 1,97549590,T,C,rs116364703,1-97549590-T-C,,,-7.0,-7.0,0,0,synonymous_variant,benign/likely_benign,0,normal_function,ClinVar,
142
+ 1,97549592,G,A,rs1382838576,1-97549592-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
143
+ 1,97549609,G,A,rs72549304,1-97549609-G-A,,,-7.0,-7.0,0,0,missense_variant,pathogenic/likely_pathogenic,0,no_function,ClinVar,
144
+ 1,97549640,C,T,rs1221109314,1-97549640-C-T,,,-7.0,-7.0,0,0,missense_variant,likely_benign,0,normal_function,ClinVar,
145
+ 1,97549647,A,G,,1-97549647-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
146
+ 1,97549676,G,A,rs2524373926,1-97549676-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
147
+ 1,97549695,TTCTGGGAGACCCCA,T,rs757940841,1-97549695-TTCTGGGAGACCCCA-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
148
+ 1,97549697,CT,C,rs1437370264,1-97549697-CT-C,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
149
+ 1,97549701,G,A,rs2524374167,1-97549701-G-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
150
+ 1,97549704,A,AC,rs779948148,1-97549704-A-AC,,,-7.0,-7.0,0,0,frameshift_variant,pathogenic/likely_pathogenic,1,no_function,ClinVar,
151
+ 1,97549713,G,A,rs57918000,1-97549713-G-A,,,-7.0,-7.0,0,0,synonymous_variant,benign/likely_benign,0,normal_function,ClinVar,
152
+ 1,97549723,A,ATAGGGCTC,rs2524374326,1-97549723-A-ATAGGGCTC,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
153
+ 1,97549745,C,T,rs1435774234,1-97549745-C-T,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
154
+ 1,97549746,T,C,rs1057516713,1-97549746-T-C,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
155
+ 1,97549746,T,G,rs1057516713,1-97549746-T-G,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
156
+ 1,97549850,A,T,rs61789183,1-97549850-A-T,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
157
+ 1,97549925,G,T,rs2811162,1-97549925-G-T,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
158
+ 1,97573759,C,A,rs1057516357,1-97573759-C-A,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
159
+ 1,97573782,AC,A,rs1057516761,1-97573782-AC-A,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
160
+ 1,97573787,AG,A,rs1057517189,1-97573787-AG-A,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
161
+ 1,97573788,G,A,rs780469489,1-97573788-G-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
162
+ 1,97573796,TG,T,rs2523608314,1-97573796-TG-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
163
+ 1,97573806,G,A,rs770549765,1-97573806-G-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
164
+ 1,97573819,A,G,rs200693895,1-97573819-A-G,,,-7.0,-7.0,0,0,missense_variant,likely_benign,0,normal_function,ClinVar,
165
+ 1,97573821,C,A,rs764666241,1-97573821-C-A,,,-7.0,-7.0,0,0,missense_variant,likely_benign,0,normal_function,ClinVar,
166
+ 1,97573856,C,A,rs755031341,1-97573856-C-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
167
+ 1,97573863,C,T,rs56038477,1-97573863-C-T,,,-7.0,-7.0,0,0,synonymous_variant,drug_response,0,decreased_function,CPIC,Decreased function
168
+ 1,97573919,G,T,,1-97573919-G-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
169
+ 1,97573920,TG,T,rs1553197926,1-97573920-TG-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
170
+ 1,97573932,T,C,rs753482702,1-97573932-T-C,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
171
+ 1,97573942,TCA,T,rs769925158,1-97573942-TCA-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,1,no_function,ClinVar,
172
+ 1,97573943,C,A,rs78060119,1-97573943-C-A,,,-7.0,-7.0,0,0,other,drug_response,0,no_function,CPIC,No function
173
+ 1,97573959,A,G,rs150759598,1-97573959-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
174
+ 1,97593057,C,T,rs74105265,1-97593057-C-T,,,-7.0,-7.0,0,0,intron_variant,likely_benign,0,normal_function,ClinVar,
175
+ 1,97593217,C,G,,1-97593217-C-G,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
176
+ 1,97593221,C,T,,1-97593221-C-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
177
+ 1,97593224,AG,A,rs1553201443,1-97593224-AG-A,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
178
+ 1,97593235,TTA,T,rs749571474,1-97593235-TTA-T,,,-7.0,-7.0,0,0,frameshift_variant,pathogenic/likely_pathogenic,1,no_function,ClinVar,
179
+ 1,97593274,G,A,rs779557503,1-97593274-G-A,,,-7.0,-7.0,0,0,missense_variant,likely_pathogenic,0,no_function,ClinVar,
180
+ 1,97593303,GCA,G,rs1553201476,1-97593303-GCA-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
181
+ 1,97593310,C,CA,rs1654652414,1-97593310-C-CA,,,-7.0,-7.0,0,0,other,likely_pathogenic,1,no_function,ClinVar,
182
+ 1,97593326,A,C,rs774390439,1-97593326-A-C,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
183
+ 1,97593352,G,GT,rs2523745739,1-97593352-G-GT,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
184
+ 1,97593380,G,A,rs768834079,1-97593380-G-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
185
+ 1,97593380,G,T,rs768834079,1-97593380-G-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
186
+ 1,97593389,T,C,rs577302209,1-97593389-T-C,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
187
+ 1,97594913,C,CT,rs1397160848,1-97594913-C-CT,,,-7.0,-7.0,0,0,intron_variant,likely_benign,1,normal_function,ClinVar,
188
+ 1,97594925,A,C,rs2811202,1-97594925-A-C,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
189
+ 1,97595057,A,G,rs1654782224,1-97595057-A-G,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
190
+ 1,97595106,TA,T,rs1057516711,1-97595106-TA-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
191
+ 1,97595122,G,A,rs2102259303,1-97595122-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
192
+ 1,97595138,G,A,rs2523757968,1-97595138-G-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
193
+ 1,97595167,C,G,rs1057516696,1-97595167-C-G,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
194
+ 1,97595197,G,A,rs2786491,1-97595197-G-A,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
195
+ 1,97595421,T,C,rs3790386,1-97595421-T-C,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
196
+ 1,97679054,A,G,rs112550271,1-97679054-A-G,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
197
+ 1,97679132,CA,C,rs1660305188,1-97679132-CA-C,,,-7.0,-7.0,0,0,other,pathogenic,1,no_function,ClinVar,
198
+ 1,97679138,G,A,,1-97679138-G-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
199
+ 1,97679174,G,A,rs754745863,1-97679174-G-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
200
+ 1,97679174,G,T,rs754745863,1-97679174-G-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
201
+ 1,97679183,C,T,rs2524268975,1-97679183-C-T,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
202
+ 1,97679184,T,C,rs1300669537,1-97679184-T-C,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
203
+ 1,97679300,T,C,rs3790387,1-97679300-T-C,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
204
+ 1,97691715,A,G,rs1057517065,1-97691715-A-G,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
205
+ 1,97691775,C,T,rs755416212,1-97691775-C-T,,,-7.0,-7.0,0,0,missense_variant,likely_pathogenic,0,no_function,ClinVar,
206
+ 1,97691776,G,A,rs1801266,1-97691776-G-A,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,decreased_function,CPIC,Decreased function
207
+ 1,97691782,G,A,rs2524347160,1-97691782-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
208
+ 1,97691806,G,A,rs74774246,1-97691806-G-A,,,-7.0,-7.0,0,0,intron_variant,benign/likely_benign,0,normal_function,ClinVar,
209
+ 1,97692035,C,T,rs2786511,1-97692035-C-T,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
210
+ 1,97699212,C,T,rs6668296,1-97699212-C-T,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
211
+ 1,97699350,C,A,rs867460475,1-97699350-C-A,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
212
+ 1,97699350,C,T,rs867460475,1-97699350-C-T,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
213
+ 1,97699370,C,A,rs146170505,1-97699370-C-A,,,-7.0,-7.0,0,0,other,pathogenic/likely_pathogenic,0,no_function,ClinVar,
214
+ 1,97699373,G,A,rs1220608789,1-97699373-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
215
+ 1,97699409,G,A,rs1411354209,1-97699409-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
216
+ 1,97699413,CA,C,rs2524392157,1-97699413-CA-C,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
217
+ 1,97699425,A,G,,1-97699425-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
218
+ 1,97699430,T,G,rs72549308,1-97699430-T-G,,,-7.0,-7.0,0,0,missense_variant,likely_pathogenic,0,no_function,ClinVar,
219
+ 1,97699440,A,G,rs758927521,1-97699440-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
220
+ 1,97699440,A,T,rs758927521,1-97699440-A-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
221
+ 1,97699455,AAG,A,rs2524392830,1-97699455-AAG-A,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
222
+ 1,97699461,A,G,rs149843476,1-97699461-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
223
+ 1,97699486,A,AT,rs754785410,1-97699486-A-AT,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
224
+ 1,97699506,C,T,rs6670886,1-97699506-C-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
225
+ 1,97699507,GA,G,rs1057516997,1-97699507-GA-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
226
+ 1,97699523,G,A,rs2100972370,1-97699523-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
227
+ 1,97699535,T,C,rs2297595,1-97699535-T-C,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,normal_function,CPIC,Normal function
228
+ 1,97699548,C,T,rs2100972539,1-97699548-C-T,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
229
+ 1,97699549,T,C,rs928629166,1-97699549-T-C,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
230
+ 1,97699692,A,T,rs78682297,1-97699692-A-T,,,-7.0,-7.0,0,0,intron_variant,likely_benign,0,normal_function,ClinVar,
231
+ 1,97720673,T,C,rs55684412,1-97720673-T-C,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
232
+ 1,97720861,C,A,,1-97720861-C-A,,,-7.0,-7.0,0,0,intron_variant,likely_benign,0,normal_function,ClinVar,
233
+ 1,97720906,A,T,rs1349131310,1-97720906-A-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
234
+ 1,97720909,G,C,rs72977734,1-97720909-G-C,,,-7.0,-7.0,0,0,missense_variant,benign,0,normal_function,ClinVar,
235
+ 1,97721231,G,T,rs79063448,1-97721231-G-T,,,-7.0,-7.0,0,0,intron_variant,likely_benign,0,normal_function,ClinVar,
236
+ 1,97721492,C,T,rs56276561,1-97721492-C-T,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
237
+ 1,97721509,C,A,rs1057516763,1-97721509-C-A,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
238
+ 1,97721519,A,G,rs190771411,1-97721519-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
239
+ 1,97721529,A,T,rs2101026231,1-97721529-A-T,,,-7.0,-7.0,0,0,other,pathogenic,0,no_function,ClinVar,
240
+ 1,97721530,A,G,,1-97721530-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
241
+ 1,97721548,G,GTCCC,rs2524538529,1-97721548-G-GTCCC,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
242
+ 1,97721640,GAA,G,rs2524539576,1-97721640-GAA-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
243
+ 1,97721651,C,T,rs370615432,1-97721651-C-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
244
+ 1,97721657,A,C,rs2524539741,1-97721657-A-C,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
245
+ 1,97721672,C,G,rs1057516356,1-97721672-C-G,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
246
+ 1,97740390,A,G,,1-97740390-A-G,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
247
+ 1,97740410,GATGA,G,rs72549309,1-97740410-GATGA-G,,,-7.0,-7.0,0,0,frameshift_variant,pathogenic,1,no_function,ClinVar,
248
+ 1,97740434,A,G,rs2101070143,1-97740434-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
249
+ 1,97740452,A,G,rs1056815262,1-97740452-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
250
+ 1,97740455,C,T,rs201841475,1-97740455-C-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
251
+ 1,97740456,G,A,rs568132506,1-97740456-G-A,,,-7.0,-7.0,0,0,missense_variant,pathogenic/likely_pathogenic,0,no_function,ClinVar,
252
+ 1,97828113,C,A,rs1553247675,1-97828113-C-A,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
253
+ 1,97828115,T,A,rs776692894,1-97828115-T-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
254
+ 1,97828127,GGAGAGCT,ATTG,rs2525244930,1-97828127-GGAGAGCT-ATTG,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
255
+ 1,97828139,G,A,rs141597515,1-97828139-G-A,,,-7.0,-7.0,0,0,other,pathogenic/likely_pathogenic,0,no_function,ClinVar,
256
+ 1,97828142,C,A,rs2525245079,1-97828142-C-A,,,-7.0,-7.0,0,0,other,pathogenic/likely_pathogenic,0,no_function,ClinVar,
257
+ 1,97828198,T,G,rs1669337684,1-97828198-T-G,,,-7.0,-7.0,0,0,splice_acceptor_variant,pathogenic,0,no_function,ClinVar,
258
+ 1,97828265,C,T,rs115632870,1-97828265-C-T,,,-7.0,-7.0,0,0,intron_variant,benign,0,normal_function,ClinVar,
259
+ 1,97883262,A,T,rs1057516405,1-97883262-A-T,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
260
+ 1,97883273,C,T,,1-97883273-C-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
261
+ 1,97883279,AGGATTTCT,A,rs1207177925,1-97883279-AGGATTTCT-A,,,-7.0,-7.0,0,0,other,pathogenic/likely_pathogenic,1,no_function,ClinVar,
262
+ 1,97883294,AT,G,rs2523808126,1-97883294-AT-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
263
+ 1,97883319,G,T,rs748974194,1-97883319-G-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
264
+ 1,97883329,A,,rs1801265,1-97883329-A-,,,-7.0,-7.0,0,0,other,conflicting_classifications_of_pathogenicity,1,normal_function,CPIC,Normal function
265
+ 1,97883329,A,G,rs1801265,1-97883329-A-G,,,-7.0,-7.0,0,0,missense_variant,drug_response,0,normal_function,CPIC,Normal function
266
+ 1,97883353,G,A,rs72549310,1-97883353-G-A,,,-7.0,-7.0,0,0,other,pathogenic/likely_pathogenic,0,no_function,ClinVar,
267
+ 1,97883369,G,T,rs267598790,1-97883369-G-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
268
+ 1,97883371,TACTCTAAAG,T,rs1672325016,1-97883371-TACTCTAAAG-T,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,1,no_function,ClinVar,
269
+ 1,97920902,C,T,rs774730464,1-97920902-C-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
270
+ 1,97920910,G,GC,,1-97920910-G-GC,,,-7.0,-7.0,0,0,frameshift_variant,pathogenic,1,no_function,ClinVar,
271
+ 1,97920920,C,T,rs768020954,1-97920920-C-T,,,-7.0,-7.0,0,0,missense_variant,likely_pathogenic,0,no_function,ClinVar,
272
+ 1,97920922,T,G,rs772950053,1-97920922-T-G,,,-7.0,-7.0,0,0,missense_variant,likely_pathogenic,0,no_function,ClinVar,
273
+ 1,97921165,C,T,rs72981743,1-97921165-C-T,,,-7.0,-7.0,0,0,other,benign,0,normal_function,ClinVar,
274
+ 1,97921399,A,C,rs61787828,1-97921399-A-C,,,-7.0,-7.0,0,0,other,benign,0,normal_function,ClinVar,
requirements.txt ADDED
@@ -0,0 +1,10 @@
 
 
 
 
 
 
 
 
 
 
 
1
+ pandas==2.2.2
2
+ numpy>=1.26,<2.1
3
+ scikit-learn==1.5.1
4
+ xgboost==2.1.1
5
+ lightgbm==4.5.0
6
+ joblib>=1.3
7
+ requests>=2.31
8
+ pysam==0.23.3
9
+ openpyxl>=3.1
10
+ google-cloud-storage>=2.16
run.sh ADDED
@@ -0,0 +1,29 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env bash
2
+ # DPYD baseline classifier — full pipeline (run EXPLICITLY; not part of scaffolding).
3
+ # No Vertex Workbench. Runs locally or in a short-lived Cloud Run job.
4
+ set -euo pipefail
5
+
6
+ BUCKET="${BUCKET:-gs://anukriti-ml-artifacts/dpyd-classifier}"
7
+ cd "$(dirname "$0")"
8
+
9
+ echo "[1/5] (re)pull gnomAD SAS/global AF for ALL ClinVar DPYD variants (full, uncapped)"
10
+ python -m src.fetch_gnomad --clinvar data/clinvar_dpyd.tsv --out data/gnomad_dpyd_sas.csv --cap 0
11
+
12
+ echo "[2/5] feature engineering -> training_data.csv + inference_set.csv"
13
+ python -m src.features
14
+
15
+ echo "[3/5] train RF/XGB/LightGBM + 5-fold CV (carries small-N caveat; use --force)"
16
+ python -m src.train --train data/training_data.csv --outdir . --n-splits 5 --force --upload "$BUCKET"
17
+
18
+ echo "[4/5] upload training data"
19
+ gcloud storage cp data/training_data.csv "$BUCKET/training_data.csv"
20
+
21
+ echo "[5/5] inference on candidate list (provide a REAL Scaria variant CSV)"
22
+ if [[ -f data/scaria_variants.csv ]]; then
23
+ python -m src.infer --variants data/scaria_variants.csv --models models \
24
+ --out results/scaria_variant_rankings.csv
25
+ gcloud storage cp results/scaria_variant_rankings.csv "$BUCKET/results/scaria_variant_rankings.csv"
26
+ else
27
+ echo " SKIP: data/scaria_variants.csv not present (Scaria et al. list unresolved)."
28
+ fi
29
+ echo "done."
src/features.py ADDED
@@ -0,0 +1,141 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """Feature engineering for the DPYD baseline classifier.
2
+
3
+ BASELINE SCOPE (by design): AF + CPIC/ClinVar categorical features ONLY.
4
+ No SIFT / PolyPhen / CADD / conservation — those require dbNSFP and were
5
+ explicitly dropped for this baseline. Any model trained on this matrix MUST be
6
+ labeled "baseline classifier, AF+categorical features".
7
+
8
+ Inputs:
9
+ data/clinvar_dpyd.tsv (ClinVar DPYD variants)
10
+ data/gnomad_dpyd_sas.csv (gnomAD SAS + global AF, per-variant)
11
+ data/cpic_dpyd_function.csv (CPIC v2024.01 functional labels — ground truth)
12
+
13
+ Outputs:
14
+ data/training_data.csv (labeled rows: normal/decreased/no function)
15
+ data/inference_set.csv (VUS/unknown rows excluded from training)
16
+
17
+ Labels (3-class): normal_function / decreased_function / no_function
18
+ - Primary truth: CPIC allele function table (joined on rsID).
19
+ - Fallback: ClinVar CLNSIG mapping for variants absent from CPIC.
20
+ - VUS / conflicting / unknown -> excluded from training, kept for inference.
21
+ """
22
+ from __future__ import annotations
23
+ import pandas as pd
24
+
25
+ # --- ClinVar CLNSIG -> 3-class fallback (only used when CPIC has no entry) ---
26
+ # Conservative mapping: pathogenic loss-of-function -> no_function;
27
+ # we do NOT invent a decreased_function signal from ClinVar (CPIC owns that).
28
+ CLNSIG_MAP = {
29
+ "pathogenic": "no_function",
30
+ "likely_pathogenic": "no_function",
31
+ "pathogenic/likely_pathogenic": "no_function",
32
+ "benign": "normal_function",
33
+ "likely_benign": "normal_function",
34
+ "benign/likely_benign": "normal_function",
35
+ }
36
+ EXCLUDE_CLNSIG_SUBSTR = ("uncertain", "conflicting", "not_provided", "other", "association")
37
+
38
+ MC_CONSEQUENCES = [
39
+ "missense_variant", "synonymous_variant", "frameshift_variant",
40
+ "stop_gained", "splice_donor_variant", "splice_acceptor_variant",
41
+ "intron_variant", "5_prime_UTR_variant", "3_prime_UTR_variant",
42
+ ]
43
+
44
+
45
+ def _norm_clnsig(s: str) -> str:
46
+ return (s or "").strip().lower().replace(" ", "_")
47
+
48
+
49
+ def _clnsig_label(clnsig: str):
50
+ c = _norm_clnsig(clnsig)
51
+ if any(x in c for x in EXCLUDE_CLNSIG_SUBSTR):
52
+ return None # -> inference only
53
+ return CLNSIG_MAP.get(c)
54
+
55
+
56
+ def _consequence(mc: str) -> str:
57
+ mc = (mc or "").lower()
58
+ for cq in MC_CONSEQUENCES:
59
+ if cq in mc:
60
+ return cq
61
+ return "other"
62
+
63
+
64
+ def build(clinvar="data/clinvar_dpyd.tsv",
65
+ gnomad="data/gnomad_dpyd_sas.csv",
66
+ cpic="data/cpic_dpyd_function.csv",
67
+ train_out="data/training_data.csv",
68
+ infer_out="data/inference_set.csv"):
69
+ cv = pd.read_csv(clinvar, sep="\t", dtype=str).fillna("")
70
+ gn = pd.read_csv(gnomad, dtype=str).fillna("") if _exists(gnomad) else pd.DataFrame(
71
+ columns=["rsid", "gnomad_global_af", "gnomad_sas_af", "in_gnomad"])
72
+ cp = pd.read_csv(cpic, dtype=str).fillna("")
73
+
74
+ # explode multi-allele ClinVar rows so each (pos,ref,alt) is one row
75
+ cv = cv.assign(alt=cv["alt"].str.split(",")).explode("alt")
76
+ cv["variant_id"] = "1-" + cv["pos"] + "-" + cv["ref"] + "-" + cv["alt"]
77
+
78
+ # --- join gnomAD AF on rsid (primary) then variant_id (fallback) ---
79
+ gn_af = gn[["rsid", "gnomad_global_af", "gnomad_sas_af", "in_gnomad"]].drop_duplicates("rsid")
80
+ df = cv.merge(gn_af, on="rsid", how="left")
81
+
82
+ for col in ("gnomad_global_af", "gnomad_sas_af"):
83
+ df[col] = pd.to_numeric(df[col], errors="coerce")
84
+ df["in_gnomad"] = pd.to_numeric(df["in_gnomad"], errors="coerce").fillna(0).astype(int)
85
+
86
+ # --- categorical features ---
87
+ df["consequence"] = df["mc"].map(_consequence)
88
+ df["clnsig_norm"] = df["clnsig"].map(_norm_clnsig)
89
+ df["is_indel"] = ((df["ref"].str.len() != 1) | (df["alt"].str.len() != 1)).astype(int)
90
+ # AF-derived numeric features (log10 with pseudocount; rarity is signal)
91
+ for col in ("gnomad_global_af", "gnomad_sas_af"):
92
+ df[f"log10_{col}"] = _log10_af(df[col])
93
+ df["sas_enriched"] = ((df["gnomad_sas_af"].fillna(0) > df["gnomad_global_af"].fillna(0))
94
+ & (df["gnomad_sas_af"].fillna(0) > 0)).astype(int)
95
+
96
+ # --- labels ---
97
+ cpic_lbl = cp[["rsid", "label_class", "cpic_function"]].drop_duplicates("rsid")
98
+ df = df.merge(cpic_lbl, on="rsid", how="left")
99
+ df["label_source"] = ""
100
+ df.loc[df["label_class"].notna(), "label_source"] = "CPIC"
101
+
102
+ # fallback to ClinVar where CPIC is silent
103
+ need = df["label_class"].isna()
104
+ df.loc[need, "label_class"] = df.loc[need, "clnsig"].map(_clnsig_label)
105
+ df.loc[need & df["label_class"].notna(), "label_source"] = "ClinVar"
106
+
107
+ valid = {"normal_function", "decreased_function", "no_function"}
108
+ is_train = df["label_class"].isin(valid)
109
+
110
+ feature_cols = ["chrom", "pos", "ref", "alt", "rsid", "variant_id",
111
+ "gnomad_global_af", "gnomad_sas_af", "log10_gnomad_global_af",
112
+ "log10_gnomad_sas_af", "in_gnomad", "sas_enriched",
113
+ "consequence", "clnsig_norm", "is_indel",
114
+ "label_class", "label_source", "cpic_function"]
115
+ feature_cols = [c for c in feature_cols if c in df.columns]
116
+
117
+ train = df[is_train][feature_cols].copy()
118
+ infer = df[~is_train][feature_cols].copy()
119
+ train.to_csv(train_out, index=False)
120
+ infer.to_csv(infer_out, index=False)
121
+ print(f"training rows: {len(train)} (by source: "
122
+ f"{train['label_source'].value_counts().to_dict()})")
123
+ print(f" class balance: {train['label_class'].value_counts().to_dict()}")
124
+ print(f"inference rows (VUS/unknown/no-label): {len(infer)}")
125
+ print(f"wrote {train_out}, {infer_out}")
126
+ return train, infer
127
+
128
+
129
+ def _log10_af(s):
130
+ import numpy as np
131
+ v = pd.to_numeric(s, errors="coerce").fillna(0.0).astype(float)
132
+ return (v.clip(lower=0) + 1e-7).map(lambda x: float(np.log10(x)))
133
+
134
+
135
+ def _exists(p):
136
+ import os
137
+ return os.path.exists(p)
138
+
139
+
140
+ if __name__ == "__main__":
141
+ build()
src/fetch_gnomad.py ADDED
@@ -0,0 +1,116 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """Fetch gnomAD v4 SAS + global allele frequencies for DPYD variants.
2
+
3
+ Strategy: the gnomAD GraphQL *region* query over the full DPYD gene span
4
+ (~1.3 Mb) returns HTTP 502 (gateway times out). The *per-variant* query by
5
+ variant_id (`{chrom}-{pos}-{ref}-{alt}`, GRCh38) is reliable, so we query the
6
+ union of variant_ids derived from the ClinVar DPYD pull.
7
+
8
+ This is the full-run version of the scaffolding probe; it pulls *all* ClinVar
9
+ DPYD variant_ids (no cap).
10
+
11
+ Run: python -m src.fetch_gnomad --clinvar data/clinvar_dpyd.tsv --out data/gnomad_dpyd_sas.csv
12
+ """
13
+ from __future__ import annotations
14
+ import argparse, csv, time
15
+ import requests
16
+
17
+ API = "https://gnomad.broadinstitute.org/api"
18
+ HEADERS = {"Content-Type": "application/json", "User-Agent": "anukriti-research/1.0"}
19
+
20
+ VARIANT_QUERY = """
21
+ query($vid:String!){
22
+ variant(variantId:$vid, dataset: gnomad_r4){
23
+ variant_id rsid
24
+ genome{ af populations{ id ac an } }
25
+ exome{ af populations{ id ac an } }
26
+ }
27
+ }"""
28
+
29
+
30
+ def _pop_af(block: dict | None, pop: str) -> float | None:
31
+ if not block:
32
+ return None
33
+ for p in block.get("populations") or []:
34
+ if p["id"] == pop:
35
+ return (p["ac"] / p["an"]) if p.get("an") else None
36
+ return None
37
+
38
+
39
+ def query_variant(vid: str, retries: int = 3, backoff: float = 2.0):
40
+ """Return the gnomAD variant dict, None (absent), or 'ERR' (unreachable)."""
41
+ for _ in range(retries):
42
+ try:
43
+ r = requests.post(API, json={"query": VARIANT_QUERY, "variables": {"vid": vid}},
44
+ headers=HEADERS, timeout=40)
45
+ if r.status_code == 200:
46
+ return r.json().get("data", {}).get("variant")
47
+ time.sleep(backoff)
48
+ except requests.RequestException:
49
+ time.sleep(backoff)
50
+ return "ERR"
51
+
52
+
53
+ def candidate_variant_ids(clinvar_tsv: str):
54
+ seen, out = set(), []
55
+ with open(clinvar_tsv) as f:
56
+ for row in csv.DictReader(f, delimiter="\t"):
57
+ for alt in row["alt"].split(","):
58
+ if not alt or len(row["ref"]) > 50 or len(alt) > 50:
59
+ continue
60
+ vid = f'1-{row["pos"]}-{row["ref"]}-{alt}'
61
+ if vid not in seen:
62
+ seen.add(vid)
63
+ out.append((vid, row["rsid"]))
64
+ return out
65
+
66
+
67
+ def main():
68
+ ap = argparse.ArgumentParser()
69
+ ap.add_argument("--clinvar", default="data/clinvar_dpyd.tsv")
70
+ ap.add_argument("--out", default="data/gnomad_dpyd_sas.csv")
71
+ ap.add_argument("--cap", type=int, default=0, help="0 = no cap (full pull)")
72
+ ap.add_argument("--sleep", type=float, default=0.15)
73
+ args = ap.parse_args()
74
+
75
+ cands = candidate_variant_ids(args.clinvar)
76
+ if args.cap:
77
+ cands = cands[: args.cap]
78
+ print(f"querying {len(cands)} gnomAD variants...")
79
+
80
+ cols = ["variant_id", "rsid", "chrom", "pos", "ref", "alt",
81
+ "gnomad_global_af", "gnomad_sas_af", "in_gnomad", "source_dataset"]
82
+ found = null = err = 0
83
+ with open(args.out, "w", newline="") as fh:
84
+ w = csv.DictWriter(fh, fieldnames=cols)
85
+ w.writeheader()
86
+ for vid, rsid in cands:
87
+ _, pos, ref, alt = vid.split("-", 3)
88
+ v = query_variant(vid)
89
+ if v == "ERR":
90
+ err += 1
91
+ continue
92
+ row = {"variant_id": vid, "rsid": rsid, "chrom": "1", "pos": pos,
93
+ "ref": ref, "alt": alt, "source_dataset": "gnomad_r4"}
94
+ if v is None:
95
+ null += 1
96
+ row.update(gnomad_global_af="", gnomad_sas_af="", in_gnomad=0)
97
+ else:
98
+ g, e = v.get("genome"), v.get("exome")
99
+ gaf = (g or {}).get("af")
100
+ if gaf is None and e:
101
+ gaf = e.get("af")
102
+ sas = _pop_af(g, "sas")
103
+ if sas is None:
104
+ sas = _pop_af(e, "sas")
105
+ row.update(rsid=v.get("rsid") or rsid,
106
+ gnomad_global_af=gaf if gaf is not None else "",
107
+ gnomad_sas_af=sas if sas is not None else "",
108
+ in_gnomad=1)
109
+ found += 1
110
+ w.writerow(row)
111
+ time.sleep(args.sleep)
112
+ print(f"done: in_gnomad={found} not_in_gnomad={null} errors={err} -> {args.out}")
113
+
114
+
115
+ if __name__ == "__main__":
116
+ main()
src/gcs_io.py ADDED
@@ -0,0 +1,26 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """Tiny GCS I/O helpers. Uses `gcloud storage` (gsutil-free).
2
+
3
+ Prefers the google-cloud-storage client if installed; otherwise shells out to
4
+ `gcloud storage cp`, which is available wherever gcloud is.
5
+ """
6
+ from __future__ import annotations
7
+ import subprocess, os
8
+
9
+
10
+ def upload_file(local: str, gcs_uri: str):
11
+ try:
12
+ from google.cloud import storage # type: ignore
13
+ assert gcs_uri.startswith("gs://")
14
+ bucket, _, blob = gcs_uri[5:].partition("/")
15
+ storage.Client().bucket(bucket).blob(blob).upload_from_filename(local)
16
+ except Exception:
17
+ subprocess.run(["gcloud", "storage", "cp", local, gcs_uri], check=True)
18
+
19
+
20
+ def upload_dir(local_dir: str, gcs_prefix: str):
21
+ for root, _, files in os.walk(local_dir):
22
+ for fn in files:
23
+ lp = os.path.join(root, fn)
24
+ rel = os.path.relpath(lp, local_dir)
25
+ upload_file(lp, f"{gcs_prefix}/{rel}")
26
+ print(f" uploaded {rel} -> {gcs_prefix}/{rel}")
src/infer.py ADDED
@@ -0,0 +1,146 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """Inference + ranking for a candidate DPYD variant list (e.g. Scaria et al. 2025).
2
+
3
+ Loads the 3 fitted models, scores each candidate variant, and emits a ranked
4
+ table:
5
+ variant | rsID | gnomad_sas_af | predicted_class | confidence | model_agreement
6
+
7
+ - confidence = mean of the per-model max-class probability.
8
+ - model_agreement = True iff all 3 models predict the same class.
9
+ - Variants with no gnomAD SAS data are flagged as coverage gaps (kept, not dropped).
10
+
11
+ IMPORTANT: the Scaria et al. (2025) variant list is NOT bundled here — it was
12
+ not resolvable from the task spec (the ClinVar query "DPYD[gene] AND Indian
13
+ [title]" returns nothing meaningful, and the rsIDs were "to be resolved").
14
+ Provide a real list via --variants <csv with columns: rsid[,variant_id]>.
15
+ Until then this module is wired and tested in shape only.
16
+
17
+ Run: python -m src.infer --variants data/scaria_variants.csv --models models --out results/scaria_variant_rankings.csv
18
+ """
19
+ from __future__ import annotations
20
+ import argparse, csv, os
21
+ import numpy as np
22
+ import pandas as pd
23
+
24
+ from src.features import build as build_features # reuse feature transforms
25
+ from src.fetch_gnomad import query_variant, _pop_af
26
+
27
+
28
+ def _load_models(models_dir: str):
29
+ import joblib
30
+ out = {}
31
+ for name in ("rf", "xgb", "lgbm"):
32
+ p = os.path.join(models_dir, f"{name}_model.pkl")
33
+ if os.path.exists(p):
34
+ out[name] = joblib.load(p)
35
+ if not out:
36
+ raise SystemExit(f"no models found in {models_dir} — train first")
37
+ return out
38
+
39
+
40
+ def _featurize_candidates(variants_csv: str) -> pd.DataFrame:
41
+ """variants_csv must have at least 'rsid'; optional 'variant_id','gnomad_sas_af'.
42
+ Missing gnomAD AF is fetched live per-variant."""
43
+ df = pd.read_csv(variants_csv, dtype=str).fillna("")
44
+ rows = []
45
+ for _, r in df.iterrows():
46
+ vid = r.get("variant_id", "")
47
+ sas = r.get("gnomad_sas_af", "")
48
+ gaf = r.get("gnomad_global_af", "")
49
+ in_g = 1
50
+ if vid and (sas == "" or gaf == ""):
51
+ v = query_variant(vid)
52
+ if v in (None, "ERR"):
53
+ in_g = 0
54
+ else:
55
+ g, e = v.get("genome"), v.get("exome")
56
+ gaf = (g or {}).get("af") or (e or {}).get("af") if (g or e) else ""
57
+ sas = _pop_af(g, "sas")
58
+ if sas is None:
59
+ sas = _pop_af(e, "sas")
60
+ rows.append({
61
+ "rsid": r.get("rsid", ""), "variant_id": vid,
62
+ "gnomad_global_af": gaf, "gnomad_sas_af": sas, "in_gnomad": in_g,
63
+ "consequence": r.get("consequence", "other"),
64
+ "clnsig_norm": r.get("clnsig_norm", ""),
65
+ "ref": r.get("ref", ""), "alt": r.get("alt", ""),
66
+ })
67
+ out = pd.DataFrame(rows)
68
+ out["coverage_gap"] = ((out["gnomad_sas_af"].isna()) |
69
+ (out["gnomad_sas_af"].astype(str) == "") |
70
+ (out["in_gnomad"] == 0))
71
+ return out
72
+
73
+
74
+ def _align(X_raw: pd.DataFrame, feats: list[str]) -> pd.DataFrame:
75
+ import numpy as np
76
+ num = ["gnomad_global_af", "gnomad_sas_af", "in_gnomad"]
77
+ X = X_raw.copy()
78
+ for c in num:
79
+ X[c] = pd.to_numeric(X[c], errors="coerce").fillna(0.0)
80
+ X["log10_gnomad_global_af"] = np.log10(X["gnomad_global_af"].clip(lower=0) + 1e-7)
81
+ X["log10_gnomad_sas_af"] = np.log10(X["gnomad_sas_af"].clip(lower=0) + 1e-7)
82
+ X["sas_enriched"] = ((X["gnomad_sas_af"] > X["gnomad_global_af"]) & (X["gnomad_sas_af"] > 0)).astype(int)
83
+ X["is_indel"] = ((X["ref"].str.len() != 1) | (X["alt"].str.len() != 1)).astype(int)
84
+ X = pd.concat([X, pd.get_dummies(X[["consequence", "clnsig_norm"]].astype(str),
85
+ prefix=["consequence", "clnsig_norm"])], axis=1)
86
+ for f in feats:
87
+ if f not in X.columns:
88
+ X[f] = 0
89
+ return X[feats]
90
+
91
+
92
+ def rank(variants_csv: str, models_dir="models", out="results/scaria_variant_rankings.csv"):
93
+ models = _load_models(models_dir)
94
+ cand = _featurize_candidates(variants_csv)
95
+ feats = next(iter(models.values()))["features"]
96
+ classes = next(iter(models.values()))["classes"]
97
+ X = _align(cand, feats)
98
+
99
+ per_model_pred, per_model_conf = {}, {}
100
+ for name, bundle in models.items():
101
+ m = bundle["model"]
102
+ proba = m.predict_proba(X)
103
+ idx = proba.argmax(axis=1)
104
+ per_model_pred[name] = [classes[i] for i in idx]
105
+ per_model_conf[name] = proba.max(axis=1)
106
+
107
+ n = len(cand)
108
+ results = []
109
+ for i in range(n):
110
+ preds = {k: per_model_pred[k][i] for k in models}
111
+ confs = [per_model_conf[k][i] for k in models]
112
+ agree = len(set(preds.values())) == 1
113
+ # consensus = majority vote; confidence = mean max-prob
114
+ vote = max(set(preds.values()), key=list(preds.values()).count)
115
+ results.append({
116
+ "variant": cand.iloc[i]["variant_id"] or cand.iloc[i]["rsid"],
117
+ "rsID": cand.iloc[i]["rsid"],
118
+ "gnomad_sas_af": cand.iloc[i]["gnomad_sas_af"],
119
+ "predicted_class": vote,
120
+ "confidence": round(float(np.mean(confs)), 4),
121
+ "model_agreement": bool(agree),
122
+ "per_model": ";".join(f"{k}={v}" for k, v in preds.items()),
123
+ "coverage_gap": bool(cand.iloc[i]["coverage_gap"]),
124
+ })
125
+ res = pd.DataFrame(results).sort_values("confidence", ascending=False)
126
+ os.makedirs(os.path.dirname(out), exist_ok=True)
127
+ res.to_csv(out, index=False)
128
+ gaps = res[res["coverage_gap"]]["rsID"].tolist()
129
+ print(f"ranked {len(res)} variants -> {out}")
130
+ print(f"all-3-agree: {int(res['model_agreement'].sum())} | coverage gaps (no gnomAD SAS): {len(gaps)}")
131
+ if gaps:
132
+ print("coverage-gap rsIDs:", gaps)
133
+ return res
134
+
135
+
136
+ def main():
137
+ ap = argparse.ArgumentParser()
138
+ ap.add_argument("--variants", required=True, help="CSV with at least an 'rsid' column")
139
+ ap.add_argument("--models", default="models")
140
+ ap.add_argument("--out", default="results/scaria_variant_rankings.csv")
141
+ args = ap.parse_args()
142
+ rank(args.variants, args.models, args.out)
143
+
144
+
145
+ if __name__ == "__main__":
146
+ main()
src/train.py ADDED
@@ -0,0 +1,165 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """Train the DPYD baseline classifier — RandomForest, XGBoost, LightGBM.
2
+
3
+ BASELINE: AF + CPIC/ClinVar categorical features only (no SIFT/PolyPhen/CADD).
4
+ 5-fold stratified CV. Reports accuracy, per-class F1, and macro one-vs-rest
5
+ AUC-ROC. Persists fitted models (refit on full data) + cv_metrics.json.
6
+
7
+ HONESTY GUARD: the CPIC ground-truth set for DPYD is tiny (~13 alleles). With
8
+ 3 classes and AF+categorical features only, CV metrics on this set are
9
+ indicative, not validating. The guard below refuses to emit metrics silently
10
+ if any class has fewer than MIN_PER_CLASS examples — it prints a loud caveat
11
+ and (optionally) reduces n_splits. This mirrors the platform invariant:
12
+ "refuse honestly when evidence is thin."
13
+
14
+ Run: python -m src.train --train data/training_data.csv --outdir . --upload <bucket>
15
+ DO NOT run as part of scaffolding — invoked explicitly at training time.
16
+ """
17
+ from __future__ import annotations
18
+ import argparse, json, sys
19
+ from collections import Counter
20
+
21
+ import numpy as np
22
+ import pandas as pd
23
+
24
+ CLASSES = ["normal_function", "decreased_function", "no_function"]
25
+ MIN_PER_CLASS = 5 # below this, CV is noise; we say so loudly.
26
+
27
+ NUMERIC = ["gnomad_global_af", "gnomad_sas_af", "log10_gnomad_global_af",
28
+ "log10_gnomad_sas_af", "in_gnomad", "sas_enriched", "is_indel"]
29
+ CATEGORICAL = ["consequence", "clnsig_norm"]
30
+
31
+
32
+ def _xy(df: pd.DataFrame):
33
+ df = df[df["label_class"].isin(CLASSES)].copy()
34
+ X_num = df[NUMERIC].apply(pd.to_numeric, errors="coerce").fillna(0.0)
35
+ X_cat = pd.get_dummies(df[CATEGORICAL].astype(str), prefix=CATEGORICAL)
36
+ X = pd.concat([X_num, X_cat], axis=1)
37
+ y = df["label_class"].astype("category")
38
+ return X, y, list(X.columns)
39
+
40
+
41
+ def _models():
42
+ from sklearn.ensemble import RandomForestClassifier
43
+ models = {"rf": RandomForestClassifier(n_estimators=400, random_state=42,
44
+ class_weight="balanced", n_jobs=-1)}
45
+ try:
46
+ from xgboost import XGBClassifier
47
+ models["xgb"] = XGBClassifier(n_estimators=400, max_depth=4, learning_rate=0.05,
48
+ subsample=0.9, colsample_bytree=0.9,
49
+ objective="multi:softprob", random_state=42,
50
+ eval_metric="mlogloss", tree_method="hist")
51
+ except ImportError:
52
+ print("WARN: xgboost not installed — skipping xgb")
53
+ try:
54
+ from lightgbm import LGBMClassifier
55
+ models["lgbm"] = LGBMClassifier(n_estimators=400, max_depth=-1, learning_rate=0.05,
56
+ subsample=0.9, colsample_bytree=0.9,
57
+ class_weight="balanced", random_state=42, verbose=-1)
58
+ except ImportError:
59
+ print("WARN: lightgbm not installed — skipping lgbm")
60
+ return models
61
+
62
+
63
+ def cross_validate(X, y, n_splits=5):
64
+ from sklearn.model_selection import StratifiedKFold
65
+ from sklearn.metrics import f1_score, accuracy_score, roc_auc_score
66
+ from sklearn.preprocessing import label_binarize
67
+
68
+ classes_present = list(y.cat.categories)
69
+ skf = StratifiedKFold(n_splits=n_splits, shuffle=True, random_state=42)
70
+ out = {}
71
+ for name, model in _models().items():
72
+ accs, f1s, aucs = [], {c: [] for c in classes_present}, []
73
+ for tr, te in skf.split(X, y):
74
+ m = _clone(model)
75
+ m.fit(X.iloc[tr], y.iloc[tr].cat.codes)
76
+ pred = m.predict(X.iloc[te])
77
+ ytrue = y.iloc[te].cat.codes.to_numpy()
78
+ accs.append(accuracy_score(ytrue, pred))
79
+ f1c = f1_score(ytrue, pred, average=None,
80
+ labels=list(range(len(classes_present))), zero_division=0)
81
+ for i, c in enumerate(classes_present):
82
+ f1s[c].append(float(f1c[i]))
83
+ try:
84
+ proba = m.predict_proba(X.iloc[te])
85
+ yb = label_binarize(ytrue, classes=list(range(len(classes_present))))
86
+ aucs.append(float(roc_auc_score(yb, proba, average="macro", multi_class="ovr")))
87
+ except Exception:
88
+ pass
89
+ out[name] = {
90
+ "accuracy_mean": float(np.mean(accs)), "accuracy_std": float(np.std(accs)),
91
+ "f1_per_class": {c: float(np.mean(v)) for c, v in f1s.items()},
92
+ "auc_roc_macro_ovr": float(np.mean(aucs)) if aucs else None,
93
+ "n_splits": n_splits,
94
+ }
95
+ return out, classes_present
96
+
97
+
98
+ def _clone(m):
99
+ from sklearn.base import clone
100
+ return clone(m)
101
+
102
+
103
+ def main():
104
+ ap = argparse.ArgumentParser()
105
+ ap.add_argument("--train", default="data/training_data.csv")
106
+ ap.add_argument("--outdir", default=".")
107
+ ap.add_argument("--n-splits", type=int, default=5)
108
+ ap.add_argument("--upload", default="", help="gs:// bucket prefix to upload to (optional)")
109
+ ap.add_argument("--force", action="store_true", help="train even if class counts are below the guard")
110
+ args = ap.parse_args()
111
+
112
+ df = pd.read_csv(args.train)
113
+ X, y, feats = _xy(df)
114
+ counts = Counter(y)
115
+ print(f"training rows: {len(X)} | features: {len(feats)} | class counts: {dict(counts)}")
116
+
117
+ # --- honesty guard ---
118
+ too_small = [c for c in CLASSES if counts.get(c, 0) < MIN_PER_CLASS]
119
+ n_splits = args.n_splits
120
+ if too_small:
121
+ msg = (f"\n*** EVIDENCE-THIN WARNING ***\n"
122
+ f"Classes below MIN_PER_CLASS={MIN_PER_CLASS}: {too_small}.\n"
123
+ f"5-fold CV on this set produces indicative, NOT validating, metrics.\n"
124
+ f"Report all numbers as 'baseline classifier, AF+categorical features, "
125
+ f"small-N (illustrative)'.\n")
126
+ print(msg)
127
+ n_splits = max(2, min(n_splits, min(counts.values())))
128
+ if not args.force:
129
+ print("Refusing to silently emit CV metrics. Re-run with --force to proceed "
130
+ "(metrics will carry the small-N caveat in cv_metrics.json).")
131
+ sys.exit(2)
132
+
133
+ metrics, classes_present = cross_validate(X, y, n_splits=n_splits)
134
+ payload = {
135
+ "model_label": "baseline classifier, AF+categorical features (no SIFT/PolyPhen/CADD)",
136
+ "feature_columns": feats,
137
+ "classes": classes_present,
138
+ "class_counts": dict(counts),
139
+ "evidence_caveat": ("small-N (illustrative)" if too_small else "ok"),
140
+ "cv": metrics,
141
+ }
142
+ import os
143
+ os.makedirs(f"{args.outdir}/results", exist_ok=True)
144
+ os.makedirs(f"{args.outdir}/models", exist_ok=True)
145
+ with open(f"{args.outdir}/results/cv_metrics.json", "w") as f:
146
+ json.dump(payload, f, indent=2)
147
+ print("wrote results/cv_metrics.json")
148
+
149
+ # refit on full data + persist
150
+ import joblib
151
+ for name, model in _models().items():
152
+ m = _clone(model)
153
+ m.fit(X, y.cat.codes)
154
+ joblib.dump({"model": m, "features": feats, "classes": classes_present},
155
+ f"{args.outdir}/models/{name}_model.pkl")
156
+ print(f"saved models/{name}_model.pkl")
157
+
158
+ if args.upload:
159
+ from src.gcs_io import upload_dir
160
+ upload_dir(f"{args.outdir}/models", f"{args.upload}/models")
161
+ upload_dir(f"{args.outdir}/results", f"{args.upload}/results")
162
+
163
+
164
+ if __name__ == "__main__":
165
+ main()
v1/models/lgbm_model.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:752bbf284bbf9e8d91257c0ce5a1175677524eb2a7cb3bfb06a35e1f8b39a06e
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+ size 1151697
v1/models/rf_model.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:af6d6892bb221baf2776f260c86cb983fbcfba377ecc319bcf92d8940c9af57c
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+ size 1443371
v1/models/xgb_model.pkl ADDED
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:84548eff770f038f9b36b492a7079fde59a6c3b8ce7682027f69b3809c4fc622
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+ size 1001514
v1/results/cv_metrics.json ADDED
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1
+ {
2
+ "model_label": "baseline classifier, AF+categorical features (no SIFT/PolyPhen/CADD)",
3
+ "feature_columns": [
4
+ "gnomad_global_af",
5
+ "gnomad_sas_af",
6
+ "log10_gnomad_global_af",
7
+ "log10_gnomad_sas_af",
8
+ "in_gnomad",
9
+ "sas_enriched",
10
+ "is_indel",
11
+ "consequence_frameshift_variant",
12
+ "consequence_intron_variant",
13
+ "consequence_missense_variant",
14
+ "consequence_other",
15
+ "consequence_splice_acceptor_variant",
16
+ "consequence_splice_donor_variant",
17
+ "consequence_synonymous_variant",
18
+ "clnsig_norm_benign",
19
+ "clnsig_norm_benign/likely_benign",
20
+ "clnsig_norm_conflicting_classifications_of_pathogenicity",
21
+ "clnsig_norm_drug_response",
22
+ "clnsig_norm_likely_benign",
23
+ "clnsig_norm_likely_pathogenic",
24
+ "clnsig_norm_pathogenic",
25
+ "clnsig_norm_pathogenic/likely_pathogenic",
26
+ "clnsig_norm_uncertain_significance"
27
+ ],
28
+ "classes": [
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+ "decreased_function",
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+ "no_function",
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+ "normal_function"
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+ ],
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+ "class_counts": {
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+ "no_function": 150,
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+ "decreased_function": 4
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+ },
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+ "evidence_caveat": "small-N (illustrative)",
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+ "cv": {
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+ "rf": {
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+ "accuracy_mean": 0.9744245524296675,
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+ "accuracy_std": 0.011953273079181547,
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+ "f1_per_class": {
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+ "no_function": 0.9899964899964899,
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+ },
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+ "auc_roc_macro_ovr": 0.9910424325656911,
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+ },
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+ "xgb": {
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+ "accuracy_mean": 0.9743712702472294,
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+ "accuracy_std": 0.012162701272040334,
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+ "f1_per_class": {
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+ },
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+ "auc_roc_macro_ovr": 0.9943319436741421,
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+ },
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+ "lgbm": {
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+ "accuracy_mean": 0.9560954816709293,
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+ "n_splits": 4
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+ }
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+ }
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+ }
v1/results/scaria_variant_rankings.csv ADDED
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+ variant,rsID,gnomad_sas_af,predicted_class,confidence,model_agreement,per_model,coverage_gap
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1
+ chrom,pos,ref,alt,rsid,variant_id,gnomad_global_af,gnomad_sas_af,log10_gnomad_global_af,log10_gnomad_sas_af,in_gnomad,sas_enriched,consequence,clnsig_norm,is_indel,label_class,label_source,cpic_function
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+ 1,97234956,AGGT,GC,rs1057516510,1-97234956-AGGT-GC,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
52
+ 1,97234995,C,G,,1-97234995-C-G,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
53
+ 1,97235033,C,T,rs12137711,1-97235033-C-T,0.0946666666666666,0.2196435971819312,-1.0238024559110908,-0.6582812545811391,1,1,intron_variant,benign,0,normal_function,ClinVar,
54
+ 1,97305252,C,T,rs369672458,1-97305252-C-T,6.583798588433583e-06,0.0,-5.174976645740021,-7.0,1,0,intron_variant,likely_benign,0,normal_function,ClinVar,
55
+ 1,97305258,C,T,rs2101035489,1-97305258-C-T,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
56
+ 1,97305271,C,CT,rs1057516828,1-97305271-C-CT,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
57
+ 1,97305275,T,C,,1-97305275-T-C,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
58
+ 1,97305275,T,G,rs772853110,1-97305275-T-G,6.584665630679274e-06,0.0,-5.174920311421099,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
59
+ 1,97305283,G,A,rs759372918,1-97305283-G-A,5.271481286241434e-05,0.0,-4.277244254697665,-7.0,1,0,other,pathogenic/likely_pathogenic,0,no_function,ClinVar,
60
+ 1,97305335,C,G,rs1397691452,1-97305335-C-G,6.582758439096319e-06,0.0,-5.175044236985472,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
61
+ 1,97305348,GT,G,rs1558014211,1-97305348-GT-G,8.901341637600363e-06,0.0,-5.045692754740495,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
62
+ 1,97305351,T,TTGGTG,,1-97305351-T-TTGGTG,,,-7.0,-7.0,0,0,frameshift_variant,pathogenic,1,no_function,ClinVar,
63
+ 1,97305364,C,T,rs1801160,1-97305364-C-T,0.0400763358778625,0.0930087390761548,-1.3971109085830247,-1.0314757763967597,1,1,missense_variant,drug_response,0,decreased_function,CPIC,Decreased function
64
+ 1,97305381,A,G,rs74104343,1-97305381-A-G,0.0014666228214403,0.0,-2.833651950568841,-7.0,1,0,intron_variant,benign/likely_benign,0,normal_function,ClinVar,
65
+ 1,97306173,T,C,rs746718279,1-97306173-T-C,6.5799863136284674e-06,0.0,-5.175224427333095,-7.0,1,0,intron_variant,likely_benign,0,normal_function,ClinVar,
66
+ 1,97306175,ACCTT,A,rs1553251903,1-97306175-ACCTT-A,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,1,no_function,ClinVar,
67
+ 1,97306176,C,T,,1-97306176-C-T,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
68
+ 1,97306177,CT,C,rs1553251907,1-97306177-CT-C,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
69
+ 1,97306209,TC,T,rs2525218019,1-97306209-TC-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
70
+ 1,97306210,CA,C,rs1165702486,1-97306210-CA-C,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
71
+ 1,97306220,TG,T,rs1064796552,1-97306220-TG-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
72
+ 1,97306241,A,T,rs753891721,1-97306241-A-T,6.579553379916571e-06,0.0,-5.1752525751175975,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
73
+ 1,97306265,C,T,rs753296078,1-97306265-C-T,6.5818918990074505e-06,0.0,-5.175100554744628,-7.0,1,0,other,likely_pathogenic,0,no_function,ClinVar,
74
+ 1,97306291,C,A,rs1667161380,1-97306291-C-A,3.4242541289656286e-06,0.0,-5.452932782771859,-7.0,1,0,other,likely_pathogenic,0,no_function,ClinVar,
75
+ 1,97306298,C,A,rs2525218826,1-97306298-C-A,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
76
+ 1,97306299,T,C,rs2525218835,1-97306299-T-C,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
77
+ 1,97306391,C,A,rs7556439,1-97306391-C-A,0.2420123798235216,0.318954790543343,-0.6161622382396346,-0.49627073441427594,1,1,intron_variant,benign,0,normal_function,ClinVar,
78
+ 1,97373297,G,A,rs74105115,1-97373297-G-A,0.0171731903767064,0.0002072968490878,-1.7651464866945394,-3.683197845990258,1,0,intron_variant,benign,0,normal_function,ClinVar,
79
+ 1,97373298,C,T,rs55652347,1-97373298-C-T,0.105492715353591,0.2627752388865808,-0.9767771172244941,-0.5804153951549818,1,1,intron_variant,benign,0,normal_function,ClinVar,
80
+ 1,97373331,T,C,rs11582179,1-97373331-T-C,0.1949429787681312,0.1883547451305429,-0.7100921793329724,-0.7250232037782348,1,0,intron_variant,benign,0,normal_function,ClinVar,
81
+ 1,97373404,C,T,rs115139529,1-97373404-C-T,0.0068892595851995,0.0,-2.161821146966191,-7.0,1,0,intron_variant,likely_benign,0,normal_function,ClinVar,
82
+ 1,97373416,A,G,rs1879374,1-97373416-A-G,0.0732010088537424,0.0888566694283347,-1.13548234017912,-1.0513094804824106,1,1,intron_variant,benign,0,normal_function,ClinVar,
83
+ 1,97373460,A,G,rs1890138,1-97373460-A-G,0.2630921545682843,0.4262873754152824,-0.5798919373486136,-0.3702974270008529,1,1,intron_variant,benign,0,normal_function,ClinVar,
84
+ 1,97373560,C,G,rs769167857,1-97373560-C-G,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
85
+ 1,97373560,CCTGCCCACAGGCCAGG,C,rs773499329,1-97373560-CCTGCCCACAGGCCAGG-C,3.2833821462812414e-05,0.0010360547036883,-4.482357873177534,-2.9845753971562154,1,1,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
86
+ 1,97373579,C,CA,rs1057517396,1-97373579-C-CA,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
87
+ 1,97373615,AT,A,rs1057517055,1-97373615-AT-A,,,-7.0,-7.0,0,0,frameshift_variant,pathogenic,1,no_function,ClinVar,
88
+ 1,97373635,CTCCAGAA,C,rs1440380546,1-97373635-CTCCAGAA-C,4.105657733211624e-06,0.0,-5.376166074166554,-7.0,1,0,splice_acceptor_variant,likely_pathogenic,1,no_function,ClinVar,
89
+ 1,97373857,C,G,rs6699630,1-97373857-C-G,0.5052336374767943,0.6803995006242197,-0.29650765670975243,-0.16723594997826416,1,1,intron_variant,benign,0,normal_function,ClinVar,
90
+ 1,97382318,T,C,rs72728438,1-97382318-T-C,0.1919090275311419,0.3750519750519751,-0.716904368974072,-0.42590842737211176,1,1,intron_variant,benign,0,normal_function,ClinVar,
91
+ 1,97382396,AG,A,rs1057516710,1-97382396-AG-A,6.95618300326245e-07,0.0,-6.099295236056275,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
92
+ 1,97382432,G,T,rs1570632355,1-97382432-G-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
93
+ 1,97382461,T,G,rs55971861,1-97382461-T-G,0.0004734599400284,0.0,-3.3246250431104314,-7.0,1,0,missense_variant,uncertain_significance,0,no_function,CPIC,No function
94
+ 1,97382485,T,G,rs12078940,1-97382485-T-G,0.0172980146372869,0.0002072109407376,-1.7620012290817646,-3.683377777613875,1,0,intron_variant,benign,0,normal_function,ClinVar,
95
+ 1,97382584,G,T,rs56279424,1-97382584-G-T,0.1921184857811801,0.3736013261500207,-0.7164306189396455,-0.42759147460494695,1,1,intron_variant,benign,0,normal_function,ClinVar,
96
+ 1,97450056,T,TA,rs760156122,1-97450056-T-TA,2.7368317341113238e-06,0.0,-5.547166423497123,-7.0,1,0,splice_donor_variant,likely_pathogenic,1,no_function,ClinVar,
97
+ 1,97450058,C,G,rs3918290,1-97450058-C-G,6.84219169084241e-07,0.0,-6.105562546216172,-7.0,1,0,splice_donor_variant,pathogenic/likely_pathogenic,0,no_function,CPIC,No function
98
+ 1,97450058,C,T,rs3918290,1-97450058-C-T,6.84219169084241e-07,0.0,-6.105562546216172,-7.0,1,0,splice_donor_variant,drug_response,0,no_function,CPIC,No function
99
+ 1,97450067,GA,G,rs2523871765,1-97450067-GA-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
100
+ 1,97450101,C,T,rs1057516388,1-97450101-C-T,6.572634180326792e-06,0.0,-5.175702684203686,-7.0,1,0,other,likely_pathogenic,0,no_function,ClinVar,
101
+ 1,97450107,T,G,,1-97450107-T-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
102
+ 1,97450133,C,A,rs1057516671,1-97450133-C-A,2.052421583812688e-06,0.0,-5.667072661634022,-7.0,1,0,other,likely_pathogenic,0,no_function,ClinVar,
103
+ 1,97450142,GAA,G,,1-97450142-GAA-G,,,-7.0,-7.0,0,0,frameshift_variant,pathogenic,1,no_function,ClinVar,
104
+ 1,97450183,GT,G,rs2523873242,1-97450183-GT-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
105
+ 1,97450193,T,TGA,,1-97450193-T-TGA,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
106
+ 1,97450199,TG,T,rs1346124437,1-97450199-TG-T,6.571770303484353e-06,0.0,-5.175758914055936,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
107
+ 1,97515585,A,AT,rs56080540,1-97515585-A-AT,0.0834352681213747,0.1020323517212774,-1.0786498135839622,-0.9912616776303826,1,1,intron_variant,benign,1,normal_function,ClinVar,
108
+ 1,97515643,T,TA,rs145228578,1-97515643-T-TA,0.0444254198221929,0.0037359900373599,-1.3523674818211604,-2.4275826660989597,1,0,intron_variant,benign,1,normal_function,ClinVar,
109
+ 1,97515686,T,C,rs2811178,1-97515686-T-C,0.6179369597301286,0.626503525508088,-0.20905575792726389,-0.20307641144780275,1,1,intron_variant,benign,0,normal_function,ClinVar,
110
+ 1,97515687,G,A,rs2786783,1-97515687-G-A,0.1759475161048097,0.095585172844648,-0.754616612997816,-1.0196090158305862,1,0,intron_variant,benign,0,normal_function,ClinVar,
111
+ 1,97515738,GA,G,rs764584080,1-97515738-GA-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
112
+ 1,97515751,A,AG,rs1290522460,1-97515751-A-AG,1.3693021625389052e-06,0.0,-5.832888882202347,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
113
+ 1,97515763,C,T,rs2101975422,1-97515763-C-T,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
114
+ 1,97515765,T,A,rs148372305,1-97515765-T-A,0.0005325303739546,0.0,-3.2735740709711574,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
115
+ 1,97515783,T,G,rs1648178154,1-97515783-T-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
116
+ 1,97515785,G,A,rs1057516968,1-97515785-G-A,3.291335887409982e-05,0.0,-4.481310287051809,-7.0,1,0,other,pathogenic/likely_pathogenic,0,no_function,ClinVar,
117
+ 1,97515787,A,C,rs55886062,1-97515787-A-C,0.0003878262012752,0.0,-3.41125088633202,-7.0,1,0,missense_variant,drug_response,0,no_function,CPIC,No function
118
+ 1,97515794,AT,A,rs1057517018,1-97515794-AT-A,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
119
+ 1,97515795,T,C,rs780421257,1-97515795-T-C,1.0952422675895907e-05,1.1596085161649427e-05,-4.956542514788901,-4.931959478185482,1,1,synonymous_variant,likely_benign,0,normal_function,ClinVar,
120
+ 1,97515816,G,A,rs149101842,1-97515816-G-A,6.578947368421053e-06,0.0,-5.175291978858124,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
121
+ 1,97515839,T,C,rs1801159,1-97515839-T-C,0.1861216805129488,0.0963530874430169,-0.7302028014898881,-1.0161339139507528,1,0,missense_variant,drug_response,0,normal_function,CPIC,Normal function
122
+ 1,97515849,T,C,rs762029458,1-97515849-T-C,6.160847404024266e-06,0.0,-5.203366881169018,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
123
+ 1,97515855,CATTTCTACACT,C,rs2524206318,1-97515855-CATTTCTACACT-C,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
124
+ 1,97515864,A,G,rs1257539978,1-97515864-A-G,4.107254095274604e-06,0.0,-5.376001258165263,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
125
+ 1,97515865,C,T,rs1801158,1-97515865-C-T,0.013718629978429,0.0072583990045624,-1.8626860919011394,-2.1391531783952575,1,0,missense_variant,drug_response,0,normal_function,CPIC,Normal function
126
+ 1,97515891,G,C,rs752329473,1-97515891-G-C,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
127
+ 1,97515892,TAAAAGA,GT,rs2524206768,1-97515892-TAAAAGA-GT,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
128
+ 1,97515912,C,T,rs369465750,1-97515912-C-T,3.287700056548441e-05,0.0,-4.481788848300296,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
129
+ 1,97515942,C,G,rs766535034,1-97515942-C-G,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
130
+ 1,97515943,T,C,rs2524207205,1-97515943-T-C,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
131
+ 1,97515952,C,T,rs55699321,1-97515952-C-T,0.0010258568535129,0.0008295313148071,-2.9888709030402585,-3.0811148636690926,1,0,intron_variant,benign/likely_benign,0,normal_function,ClinVar,
132
+ 1,97516031,C,T,rs6657204,1-97516031-C-T,0.0237109596445663,0.0002088554720133,-1.6250490370169752,-3.6799462513015757,1,0,intron_variant,benign,0,normal_function,ClinVar,
133
+ 1,97516066,G,GA,rs141050810,1-97516066-G-GA,0.0437822606130833,0.0008309098462816,-1.3587008262857296,-3.0803938304151277,1,0,intron_variant,benign,1,normal_function,ClinVar,
134
+ 1,97516150,C,T,rs1337752,1-97516150-C-T,0.6168672792712028,0.6232876712328768,-0.20980819519140767,-0.2053113937853333,1,1,intron_variant,benign,0,normal_function,ClinVar,
135
+ 1,97549384,C,A,rs2786525,1-97549384-C-A,0.0251058124556376,0.0006231823847112,-1.600223989894209,-3.205315147022373,1,0,intron_variant,benign,0,normal_function,ClinVar,
136
+ 1,97549544,G,T,rs199469537,1-97549544-G-T,0.0004925590742516,0.0,-3.3074535135621588,-7.0,1,0,intron_variant,likely_benign,0,normal_function,ClinVar,
137
+ 1,97549559,C,T,rs1057517126,1-97549559-C-T,6.842360231107559e-07,1.1593396401409756e-05,-6.105553212687552,-4.9320593276616025,1,1,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
138
+ 1,97549565,C,T,rs138391898,1-97549565-C-T,6.1581157807875e-06,3.478018920422927e-05,-5.203556406275799,-4.457421167944463,1,1,missense_variant,likely_benign,0,normal_function,ClinVar,
139
+ 1,97549565,CG,C,rs1057516615,1-97549565-CG-C,,,-7.0,-7.0,0,0,other,likely_pathogenic,1,no_function,ClinVar,
140
+ 1,97549582,C,T,rs1214305633,1-97549582-C-T,1.1631630371418483e-05,0.0,-4.930641628795999,-7.0,1,0,other,likely_pathogenic,0,no_function,ClinVar,
141
+ 1,97549590,T,C,rs116364703,1-97549590-T-C,3.285928340474751e-05,0.0,-4.482022239230597,-7.0,1,0,synonymous_variant,benign/likely_benign,0,normal_function,ClinVar,
142
+ 1,97549592,G,A,rs1382838576,1-97549592-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
143
+ 1,97549609,G,A,rs72549304,1-97549609-G-A,4.602659021869206e-05,0.0002072968490878,-4.3360486482302125,-3.683197845990258,1,1,missense_variant,pathogenic/likely_pathogenic,0,no_function,ClinVar,
144
+ 1,97549640,C,T,rs1221109314,1-97549640-C-T,6.573584707212537e-06,0.0,-5.175640822700356,-7.0,1,0,missense_variant,likely_benign,0,normal_function,ClinVar,
145
+ 1,97549647,A,G,,1-97549647-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
146
+ 1,97549676,G,A,rs2524373926,1-97549676-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
147
+ 1,97549695,TTCTGGGAGACCCCA,T,rs757940841,1-97549695-TTCTGGGAGACCCCA-T,1.3140086461768918e-05,0.0004137360364087,-4.878109178812744,-3.3831716941149064,1,1,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
148
+ 1,97549697,CT,C,rs1437370264,1-97549697-CT-C,1.3145095564844756e-05,0.0,-4.877944903872223,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
149
+ 1,97549701,G,A,rs2524374167,1-97549701-G-A,1.368445828703425e-06,0.0,-5.833142070066697,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
150
+ 1,97549704,A,AC,rs779948148,1-97549704-A-AC,4.789639052800981e-06,0.0,-5.310723198782815,-7.0,1,0,frameshift_variant,pathogenic/likely_pathogenic,1,no_function,ClinVar,
151
+ 1,97549713,G,A,rs57918000,1-97549713-G-A,0.0071586192402669,0.0,-2.14516466996013,-7.0,1,0,synonymous_variant,benign/likely_benign,0,normal_function,ClinVar,
152
+ 1,97549723,A,ATAGGGCTC,rs2524374326,1-97549723-A-ATAGGGCTC,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
153
+ 1,97549745,C,T,rs1435774234,1-97549745-C-T,6.845948362380692e-07,0.0,-6.105354554479096,-7.0,1,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
154
+ 1,97549746,T,C,rs1057516713,1-97549746-T-C,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
155
+ 1,97549746,T,G,rs1057516713,1-97549746-T-G,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
156
+ 1,97549850,A,T,rs61789183,1-97549850-A-T,0.0862721147405335,0.048053024026512,-1.0641290528112402,-1.3182783727535599,1,0,intron_variant,benign,0,normal_function,ClinVar,
157
+ 1,97549925,G,T,rs2811162,1-97549925-G-T,0.0250726027937292,0.0006229235880398,-1.6007988473288681,-3.2054955103848166,1,0,intron_variant,benign,0,normal_function,ClinVar,
158
+ 1,97573759,C,A,rs1057516357,1-97573759-C-A,2.0530592636087037e-06,0.0,-5.666944015924765,-7.0,1,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
159
+ 1,97573782,AC,A,rs1057516761,1-97573782-AC-A,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
160
+ 1,97573787,AG,A,rs1057517189,1-97573787-AG-A,7.52704947871761e-06,0.0,-5.117643436217248,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
161
+ 1,97573788,G,A,rs780469489,1-97573788-G-A,1.3154779131258386e-05,0.0,-4.877627504662302,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
162
+ 1,97573796,TG,T,rs2523608314,1-97573796-TG-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
163
+ 1,97573806,G,A,rs770549765,1-97573806-G-A,1.3159106759833142e-05,0.0,-4.877485732518139,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
164
+ 1,97573819,A,G,rs200693895,1-97573819-A-G,5.9183270862102976e-05,0.0004144218814753,-4.227067842846302,-3.3824525392918607,1,1,missense_variant,likely_benign,0,normal_function,ClinVar,
165
+ 1,97573821,C,A,rs764666241,1-97573821-C-A,2.6308173949646157e-05,0.0,-4.578261627986945,-7.0,1,0,missense_variant,likely_benign,0,normal_function,ClinVar,
166
+ 1,97573856,C,A,rs755031341,1-97573856-C-A,6.842238506749869e-07,0.0,-6.105559953595335,-7.0,1,0,other,likely_pathogenic,0,no_function,ClinVar,
167
+ 1,97573863,C,T,rs56038477,1-97573863-C-T,0.0130954727643077,0.0161490683229813,-1.8828755019780845,-1.791849838784299,1,1,synonymous_variant,drug_response,0,decreased_function,CPIC,Decreased function
168
+ 1,97573919,G,T,,1-97573919-G-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
169
+ 1,97573920,TG,T,rs1553197926,1-97573920-TG-T,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
170
+ 1,97573932,T,C,rs753482702,1-97573932-T-C,1.7107047693080405e-05,0.0,-4.7642936375511304,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
171
+ 1,97573942,TCA,T,rs769925158,1-97573942-TCA-T,6.572374993427625e-06,0.0,-5.1757195539470695,-7.0,1,0,other,likely_pathogenic,1,no_function,ClinVar,
172
+ 1,97573943,C,A,rs78060119,1-97573943-C-A,6.572461386789352e-06,0.0,-5.1757139307743,-7.0,1,0,other,drug_response,0,no_function,CPIC,No function
173
+ 1,97573959,A,G,rs150759598,1-97573959-A-G,0.0001708525542456,0.0,-3.7671244059145796,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
174
+ 1,97593057,C,T,rs74105265,1-97593057-C-T,0.0038358467763123,0.0,-2.4161274272871487,-7.0,1,0,intron_variant,likely_benign,0,normal_function,ClinVar,
175
+ 1,97593217,C,G,,1-97593217-C-G,,,-7.0,-7.0,0,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
176
+ 1,97593221,C,T,,1-97593221-C-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
177
+ 1,97593224,AG,A,rs1553201443,1-97593224-AG-A,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
178
+ 1,97593235,TTA,T,rs749571474,1-97593235-TTA-T,2.0521913299020696e-06,0.0,-5.667119122491209,-7.0,1,0,frameshift_variant,pathogenic/likely_pathogenic,1,no_function,ClinVar,
179
+ 1,97593274,G,A,rs779557503,1-97593274-G-A,6.575140708011152e-06,0.0002075550020755,-5.175539575196536,-3.682657602971522,1,1,missense_variant,likely_pathogenic,0,no_function,ClinVar,
180
+ 1,97593303,GCA,G,rs1553201476,1-97593303-GCA-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
181
+ 1,97593310,C,CA,rs1654652414,1-97593310-C-CA,,,-7.0,-7.0,0,0,other,likely_pathogenic,1,no_function,ClinVar,
182
+ 1,97593326,A,C,rs774390439,1-97593326-A-C,1.3142331449599158e-05,0.0,-4.8780355461231455,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
183
+ 1,97593352,G,GT,rs2523745739,1-97593352-G-GT,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
184
+ 1,97593380,G,A,rs768834079,1-97593380-G-A,5.917937927406628e-05,0.0002072109407376,-4.227096352587082,-3.683377777613875,1,1,synonymous_variant,likely_benign,0,normal_function,ClinVar,
185
+ 1,97593380,G,T,rs768834079,1-97593380-G-T,5.917937927406628e-05,0.0002072109407376,-4.227096352587082,-3.683377777613875,1,1,other,likely_pathogenic,0,no_function,ClinVar,
186
+ 1,97593389,T,C,rs577302209,1-97593389-T-C,6.575486586007364e-06,0.0,-5.17551707244788,-7.0,1,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
187
+ 1,97594913,C,CT,rs1397160848,1-97594913-C-CT,0.000771116190686,0.0006558810668998,-3.1128238615588324,-3.1831086951664154,1,0,intron_variant,likely_benign,1,normal_function,ClinVar,
188
+ 1,97594925,A,C,rs2811202,1-97594925-A-C,0.1383956562921063,0.0708061002178649,-0.8588772266941276,-1.1499287112013825,1,0,intron_variant,benign,0,normal_function,ClinVar,
189
+ 1,97595057,A,G,rs1654782224,1-97595057-A-G,6.870151390656044e-07,0.0,-6.104016913448539,-7.0,1,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
190
+ 1,97595106,TA,T,rs1057516711,1-97595106-TA-T,6.842294686684484e-07,0.0,-6.105556842423929,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
191
+ 1,97595122,G,A,rs2102259303,1-97595122-G-A,8.210809804801681e-06,0.0,-5.080356656526151,-7.0,1,0,other,likely_pathogenic,0,no_function,ClinVar,
192
+ 1,97595138,G,A,rs2523757968,1-97595138-G-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
193
+ 1,97595167,C,G,rs1057516696,1-97595167-C-G,6.847664124813743e-07,0.0,-6.105259592766424,-7.0,1,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
194
+ 1,97595197,G,A,rs2786491,1-97595197-G-A,0.0160232396124978,0.0002073828287017,-1.7952469624013374,-3.683017839716601,1,0,intron_variant,benign,0,normal_function,ClinVar,
195
+ 1,97595421,T,C,rs3790386,1-97595421-T-C,0.0844570150628165,0.0664871582435791,-1.0733637575511543,-1.177261575820383,1,0,intron_variant,benign,0,normal_function,ClinVar,
196
+ 1,97679054,A,G,rs112550271,1-97679054-A-G,0.0144184030058593,0.0004142502071251,-1.841079827691737,-3.382632439725396,1,0,intron_variant,benign,0,normal_function,ClinVar,
197
+ 1,97679132,CA,C,rs1660305188,1-97679132-CA-C,6.965534535120225e-07,0.0,-6.098785075121639,-7.0,1,0,other,pathogenic,1,no_function,ClinVar,
198
+ 1,97679138,G,A,,1-97679138-G-A,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
199
+ 1,97679174,G,A,rs754745863,1-97679174-G-A,5.921598041924914e-05,0.000414937759336,-4.226828286856179,-3.3819123902149366,1,1,synonymous_variant,likely_benign,0,normal_function,ClinVar,
200
+ 1,97679174,G,T,rs754745863,1-97679174-G-T,5.921598041924914e-05,0.000414937759336,-4.226828286856179,-3.3819123902149366,1,1,other,likely_pathogenic,0,no_function,ClinVar,
201
+ 1,97679183,C,T,rs2524268975,1-97679183-C-T,3.671363074311326e-06,0.0,-5.423501655454471,-7.0,1,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
202
+ 1,97679184,T,C,rs1300669537,1-97679184-T-C,1.3142158730993151e-05,0.0,-4.878041210626181,-7.0,1,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
203
+ 1,97679300,T,C,rs3790387,1-97679300-T-C,0.0967674085369861,0.0833678971381169,-1.0142704405409984,-1.079000632019966,1,0,intron_variant,benign,0,normal_function,ClinVar,
204
+ 1,97691715,A,G,rs1057517065,1-97691715-A-G,6.845301658753498e-07,0.0,-6.105390352750935,-7.0,1,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
205
+ 1,97691775,C,T,rs755416212,1-97691775-C-T,1.026383530786716e-05,2.3191094619666047e-05,-4.98447949702284,-4.632810100297024,1,1,missense_variant,likely_pathogenic,0,no_function,ClinVar,
206
+ 1,97691776,G,A,rs1801266,1-97691776-G-A,3.950591271827017e-05,0.0,-4.402239973942371,-7.0,1,0,missense_variant,drug_response,0,decreased_function,CPIC,Decreased function
207
+ 1,97691782,G,A,rs2524347160,1-97691782-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
208
+ 1,97691806,G,A,rs74774246,1-97691806-G-A,0.0122608638485306,0.0004145936981757,-1.9114753880847557,-3.38227256427021,1,0,intron_variant,benign/likely_benign,0,normal_function,ClinVar,
209
+ 1,97692035,C,T,rs2786511,1-97692035-C-T,0.9973069546254696,1.0,-0.0011711088910513834,4.3429446044209946e-08,1,1,intron_variant,benign,0,normal_function,ClinVar,
210
+ 1,97699212,C,T,rs6668296,1-97699212-C-T,0.13290381173002,0.0934773577066888,-0.8764622363803583,-1.0292931075653304,1,0,intron_variant,benign,0,normal_function,ClinVar,
211
+ 1,97699350,C,A,rs867460475,1-97699350-C-A,6.845348517229057e-07,0.0,-6.1053877588014,-7.0,1,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
212
+ 1,97699350,C,T,rs867460475,1-97699350-C-T,6.845348517229057e-07,0.0,-6.1053877588014,-7.0,1,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
213
+ 1,97699370,C,A,rs146170505,1-97699370-C-A,6.575486586007364e-06,0.0,-5.17551707244788,-7.0,1,0,other,pathogenic/likely_pathogenic,0,no_function,ClinVar,
214
+ 1,97699373,G,A,rs1220608789,1-97699373-G-A,6.842819077232162e-07,1.1594202898550725e-05,-6.105527803435148,-4.93202937527071,1,1,other,likely_pathogenic,0,no_function,ClinVar,
215
+ 1,97699409,G,A,rs1411354209,1-97699409-G-A,4.1053374861102745e-06,3.478180216110931e-05,-5.376199145532166,-4.457401085425057,1,1,other,likely_pathogenic,0,no_function,ClinVar,
216
+ 1,97699413,CA,C,rs2524392157,1-97699413-CA-C,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
217
+ 1,97699425,A,G,,1-97699425-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
218
+ 1,97699430,T,G,rs72549308,1-97699430-T-G,6.576956973547479e-06,0.0,-5.175421422360364,-7.0,1,0,missense_variant,likely_pathogenic,0,no_function,ClinVar,
219
+ 1,97699440,A,G,rs758927521,1-97699440-A-G,4.1052869253453576e-06,0.0,-5.376204367085318,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
220
+ 1,97699440,A,T,rs758927521,1-97699440-A-T,4.1052869253453576e-06,0.0,-5.376204367085318,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
221
+ 1,97699455,AAG,A,rs2524392830,1-97699455-AAG-A,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
222
+ 1,97699461,A,G,rs149843476,1-97699461-A-G,7.231228388487884e-05,0.0,-4.140187754646791,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
223
+ 1,97699486,A,AT,rs754785410,1-97699486-A-AT,6.579380222383052e-06,0.0,-5.175263833705079,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
224
+ 1,97699506,C,T,rs6670886,1-97699506-C-T,0.0006509218104831,0.0,-3.186404461487433,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
225
+ 1,97699507,GA,G,rs1057516997,1-97699507-GA-G,6.843062571595542e-07,0.0,-6.105514320194517,-7.0,1,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
226
+ 1,97699523,G,A,rs2100972370,1-97699523-G-A,,,-7.0,-7.0,0,0,other,likely_pathogenic,0,no_function,ClinVar,
227
+ 1,97699535,T,C,rs2297595,1-97699535-T-C,0.0801614536083829,0.0732061385317295,-1.09603387434847,-1.1354519074052951,1,0,missense_variant,drug_response,0,normal_function,CPIC,Normal function
228
+ 1,97699548,C,T,rs2100972539,1-97699548-C-T,6.844411469590964e-07,0.0,-6.105439633988698,-7.0,1,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
229
+ 1,97699549,T,C,rs928629166,1-97699549-T-C,,,-7.0,-7.0,0,0,splice_acceptor_variant,likely_pathogenic,0,no_function,ClinVar,
230
+ 1,97699692,A,T,rs78682297,1-97699692-A-T,0.0043631966986897,0.0002076411960132,-2.3601852545303355,-3.6824773723761233,1,0,intron_variant,likely_benign,0,normal_function,ClinVar,
231
+ 1,97720673,T,C,rs55684412,1-97720673-T-C,0.1242962435557665,0.0970954356846473,-0.9055416468765418,-1.0128007378787587,1,0,intron_variant,benign,0,normal_function,ClinVar,
232
+ 1,97720861,C,A,,1-97720861-C-A,,,-7.0,-7.0,0,0,intron_variant,likely_benign,0,normal_function,ClinVar,
233
+ 1,97720906,A,T,rs1349131310,1-97720906-A-T,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
234
+ 1,97720909,G,C,rs72977734,1-97720909-G-C,0.0054447418032246,0.0002079002079002,-2.264014733903556,-3.6819362309513513,1,0,missense_variant,benign,0,normal_function,ClinVar,
235
+ 1,97721231,G,T,rs79063448,1-97721231-G-T,0.0112471338586827,0.0004142502071251,-1.9489542746747777,-3.382632439725396,1,0,intron_variant,likely_benign,0,normal_function,ClinVar,
236
+ 1,97721492,C,T,rs56276561,1-97721492-C-T,0.0132567767113173,0.0199252801992528,-1.8775587826290765,-1.7005933830127946,1,1,intron_variant,benign,0,normal_function,ClinVar,
237
+ 1,97721509,C,A,rs1057516763,1-97721509-C-A,6.5970023221448175e-06,0.0,-5.174119550474825,-7.0,1,0,splice_donor_variant,likely_pathogenic,0,no_function,ClinVar,
238
+ 1,97721519,A,G,rs190771411,1-97721519-A-G,7.245804020762522e-05,0.0,-4.13931445608176,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
239
+ 1,97721529,A,T,rs2101026231,1-97721529-A-T,,,-7.0,-7.0,0,0,other,pathogenic,0,no_function,ClinVar,
240
+ 1,97721530,A,G,,1-97721530-A-G,,,-7.0,-7.0,0,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
241
+ 1,97721548,G,GTCCC,rs2524538529,1-97721548-G-GTCCC,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
242
+ 1,97721640,GAA,G,rs2524539576,1-97721640-GAA-G,,,-7.0,-7.0,0,0,frameshift_variant,likely_pathogenic,1,no_function,ClinVar,
243
+ 1,97721651,C,T,rs370615432,1-97721651-C-T,6.594305158065494e-06,0.0,-5.1742944943321,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
244
+ 1,97721657,A,C,rs2524539741,1-97721657-A-C,6.852187355247542e-07,0.0,-6.105009346568283,-7.0,1,0,synonymous_variant,likely_benign,0,normal_function,ClinVar,
245
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+ 1-97373592-C-T,c.2027G>A,0.0006226650062266501,no_function,0.908,True,rf=no_function;xgb=no_function;lgbm=no_function,False
21
+ 1-97721503-T-C,c.483+7A>G,0.0,no_function,0.908,True,rf=no_function;xgb=no_function;lgbm=no_function,False
22
+ 1-97883319-G-A,c.95C>T,0.00041476565740356696,no_function,0.9078,True,rf=no_function;xgb=no_function;lgbm=no_function,False
23
+ 1-97573870-C-T,c.1229G>A,0.00041476565740356696,no_function,0.9062,True,rf=no_function;xgb=no_function;lgbm=no_function,False
24
+ 1-97193124-G-A,c.2567C>T,0.0008285004142502071,no_function,0.893,True,rf=no_function;xgb=no_function;lgbm=no_function,False
25
+ 1-97883328-C-T,c.86G>A,0.00041476565740356696,no_function,0.8865,True,rf=no_function;xgb=no_function;lgbm=no_function,False
26
+ 1-97079149-G-A,c.2908-3C>T,0.0012437810945273632,no_function,0.7818,True,rf=no_function;xgb=no_function;lgbm=no_function,False