source_index stringlengths 7 9 | label stringclasses 2
values | prompt stringlengths 17.2k 17.2k | completion stringlengths 2.11k 3.15k | prediction stringclasses 2
values | is_correct bool 1
class | model stringclasses 1
value | finish_reason stringclasses 1
value | prompt_tokens int64 7.19k 7.47k | completion_tokens int64 550 839 | reasoning_tokens int64 4.26k 43.1k | total_tokens int64 12.3k 51.1k |
|---|---|---|---|---|---|---|---|---|---|---|---|
00000/149 | benign | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 4159, using 1-based indexing relative to the sequences shown. At this position, the reference allele C... | To determine whether the single-nucleotide variant (SNV) is **benign** or **pathogenic**, we perform a step-by-step genomic analysis of the reference and alternate DNA sequences provided.
---
### Step 1: Identify the Variant and Its Genomic Position
By aligning the provided **Reference DNA sequence** and **Alternate... | benign | true | gemini-3.6-flash | stop | 7,393 | 697 | 35,117 | 43,207 |
00000/278 | benign | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 7663, using 1-based indexing relative to the sequences shown. At this position, the reference allele G... | To determine whether the single-nucleotide variant (SNV) is **benign** or **pathogenic**, we analyze its genomic context and potential impact on gene function and protein expression.
---
### Step 1: Identify the Location of the Variant
1. **Variant Position**: The reference and alternate sequences differ at position ... | benign | true | gemini-3.6-flash | stop | 7,271 | 601 | 14,363 | 22,235 |
00000/384 | benign | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 4841, using 1-based indexing relative to the sequences shown. At this position, the reference allele C... | To determine whether the single-nucleotide variant (SNV) is **benign** or **pathogenic**, we perform a step-by-step analysis of the sequence context, variant location, and potential functional impact.
---
### Step 1: Variant Identification and Localization
1. **Sequence Comparison**: Comparing the provided `Reference... | benign | true | gemini-3.6-flash | stop | 7,331 | 550 | 17,153 | 25,034 |
00000/405 | benign | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 4167, using 1-based indexing relative to the sequences shown. At this position, the reference allele G... | To classify the given human single-nucleotide variant (SNV), we perform a step-by-step genomic and bioinformatic analysis of the sequence provided.
---
### Step 1: Sequence Alignment and Gene Identification
1. **Gene Identification:**
By translating the downstream coding sequence from the splice acceptor site `CA... | benign | true | gemini-3.6-flash | stop | 7,241 | 761 | 25,019 | 33,021 |
00000/559 | benign | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 1723, using 1-based indexing relative to the sequences shown. At this position, the reference allele T... | To determine the pathogenicity of the given single-nucleotide variant (SNV), we analyze the genomic context, position, reading frames, and functional impact on the corresponding human gene.
---
### Step 1: Sequence Alignment & Variant Identification
Comparing the reference and alternate DNA sequences provided:
* **P... | benign | true | gemini-3.6-flash | stop | 7,193 | 653 | 43,060 | 50,906 |
00000/81 | benign | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 6023, using 1-based indexing relative to the sequences shown. At this position, the reference allele G... | To classify the human single-nucleotide variant (SNV) as either **benign** or **pathogenic**, we perform a sequence alignment, context analysis, functional impact assessment, and application of standard clinical genetics criteria (such as ACMG/AMP variant interpretation guidelines).
---
### Step 1: Sequence Compariso... | benign | true | gemini-3.6-flash | stop | 7,323 | 774 | 30,012 | 38,109 |
00000/9 | benign | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 4177, using 1-based indexing relative to the sequences shown. At this position, the reference allele A... | To classify the given single-nucleotide variant (SNV) as either **benign** or **pathogenic**, we perform a step-by-step genomic sequence analysis:
---
### Step 1: Locate and Extract the Variant
By comparing the provided reference and alternate DNA sequences:
* **Reference allele at position 4177:** `A`
* **Alternate ... | benign | true | gemini-3.6-flash | stop | 7,305 | 718 | 32,382 | 40,405 |
00000/920 | benign | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 1309, using 1-based indexing relative to the sequences shown. At this position, the reference allele C... | To determine whether the single-nucleotide variant (SNV) is **benign** or **pathogenic**, we perform a step-by-step analysis of the sequence context, codon change, and functional impact relative to standard variant interpretation guidelines (ACMG/AMP criteria).
---
### Step 1: Identification of the Variant
- **Locati... | benign | true | gemini-3.6-flash | stop | 7,473 | 816 | 42,860 | 51,149 |
00000/960 | benign | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 5152, using 1-based indexing relative to the sequences shown. At this position, the reference allele T... | To classify the given human single-nucleotide variant (SNV), we perform a step-by-step genomic sequence analysis, mapping, and functional evaluation:
### 1. Gene and Sequence Identification
By examining the provided reference DNA sequence, we identify distinct exon-intron structures. Specifically, around position 4100... | benign | true | gemini-3.6-flash | stop | 7,341 | 630 | 37,631 | 45,602 |
00000/986 | benign | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 4784, using 1-based indexing relative to the sequences shown. At this position, the reference allele T... | To determine whether the given single-nucleotide variant (SNV) is **benign** or **pathogenic**, we perform a detailed analysis of the sequence context, reading frames, genomic features, and potential functional impacts.
---
### Step 1: Identify the Variant Location and Local Context
From the provided sequences:
- **... | benign | true | gemini-3.6-flash | stop | 7,335 | 724 | 17,449 | 25,508 |
00000/14 | pathogenic | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 7542, using 1-based indexing relative to the sequences shown. At this position, the reference allele G... | To determine whether the given human single-nucleotide variant (SNV) is **benign** or **pathogenic**, we analyze the provided reference and alternate DNA sequences step by step:
---
### Step 1: Locate the Variant
Comparing the reference and alternate DNA sequences around position 7542:
* **Reference sequence region:... | pathogenic | true | gemini-3.6-flash | stop | 7,367 | 682 | 4,259 | 12,308 |
00000/196 | pathogenic | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 4302, using 1-based indexing relative to the sequences shown. At this position, the reference allele C... | To classify the given human single-nucleotide variant (SNV), we perform a step-by-step analysis of the nucleotide sequences, the coding frame, and the predicted protein product effect.
---
### Step 1: Identify the Nucleotide Change
Comparing the provided **Reference** and **Alternate** DNA sequences at position 4302 ... | pathogenic | true | gemini-3.6-flash | stop | 7,421 | 682 | 11,328 | 19,431 |
00000/213 | pathogenic | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 4942, using 1-based indexing relative to the sequences shown. At this position, the reference allele C... | To determine whether the given single-nucleotide variant (SNV) is **benign** or **pathogenic**, we perform a systematic analysis of the gene context, reading frame, transcript direction, and functional impact of the nucleotide change.
---
### Step 1: Sequence Alignment and Variant Identification
Comparing the referen... | pathogenic | true | gemini-3.6-flash | stop | 7,273 | 814 | 32,511 | 40,598 |
00000/268 | pathogenic | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 2442, using 1-based indexing relative to the sequences shown. At this position, the reference allele C... | To determine whether the given single-nucleotide variant (SNV) is benign or pathogenic, we analyze the sequence context, identify the affected gene, determine the reading frame, and assess the functional impact of the nucleotide change.
---
### Step 1: Gene Identification
By translating several exonic regions contain... | pathogenic | true | gemini-3.6-flash | stop | 7,341 | 731 | 11,483 | 19,555 |
00000/284 | pathogenic | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 7668, using 1-based indexing relative to the sequences shown. At this position, the reference allele G... | To determine whether the single-nucleotide variant (SNV) is **benign** or **pathogenic**, we perform a step-by-step genomic sequence and functional impact analysis.
---
### Step 1: Variant Identification and Alignment
Comparing the provided reference DNA sequence and the alternate DNA sequence:
- **Variant Position**... | pathogenic | true | gemini-3.6-flash | stop | 7,387 | 769 | 37,573 | 45,729 |
00000/321 | pathogenic | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 4314, using 1-based indexing relative to the sequences shown. At this position, the reference allele C... | To classify the given human single-nucleotide variant (SNV), we perform a step-by-step genomic sequence analysis, codon alignment, amino acid translation, and clinical impact assessment based on standard ACMG/AMP (American College of Medical Genetics and Genomics / Association for Molecular Pathology) guidelines.
---
... | pathogenic | true | gemini-3.6-flash | stop | 7,389 | 839 | 10,160 | 18,388 |
00000/377 | pathogenic | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 4854, using 1-based indexing relative to the sequences shown. At this position, the reference allele G... | To classify the given human single-nucleotide variant (SNV) as either **benign** or **pathogenic**, we perform a step-by-step sequence alignment, structural genomic analysis, and functional impact assessment according to standard clinical genetics guidelines (ACMG/AMP).
---
### Step 1: Variant Identification and Sequ... | pathogenic | true | gemini-3.6-flash | stop | 7,343 | 730 | 9,979 | 18,052 |
00000/608 | pathogenic | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 3514, using 1-based indexing relative to the sequences shown. At this position, the reference allele G... | To determine whether the given single-nucleotide variant (SNV) is **benign** or **pathogenic**, we analyze the genomic context of the reference sequence and the precise location and nature of the mutation.
---
### Step 1: Identify the Location and Genomic Context of the Variant
By comparing the reference sequence wit... | pathogenic | true | gemini-3.6-flash | stop | 7,300 | 577 | 4,895 | 12,772 |
00000/700 | pathogenic | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 5932, using 1-based indexing relative to the sequences shown. At this position, the reference allele G... | To classify the given human single-nucleotide variant (SNV), we perform a step-by-step sequence analysis:
### 1. Identify Variant Location and Nucleotide Change
- **Position**: 5932 (1-based indexing)
- **Reference Allele**: `G`
- **Alternate Allele**: `A`
Comparing the local reference sequence surrounding position 5... | pathogenic | true | gemini-3.6-flash | stop | 7,409 | 578 | 35,071 | 43,058 |
00000/731 | pathogenic | Given a human single-nucleotide variant and its surrounding reference DNA sequence, classify the variant as either benign or pathogenic.
The reference and alternate sequences differ by a single nucleotide at position 6692, using 1-based indexing relative to the sequences shown. At this position, the reference allele A... | To classify the given human single-nucleotide variant (SNV), we perform a step-by-step genomic and functional analysis:
### 1. Gene Identification
By matching the reference DNA sequence against standard reference genomes (GRCh38/hg38), the sequence corresponds to the human **APC** (*Adenomatous Polyposis Coli*) gene, ... | pathogenic | true | gemini-3.6-flash | stop | 7,283 | 570 | 7,612 | 15,465 |
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