task_categories:
- zero-shot-classification
pretty_name: ClinVar
size_categories:
- 100K<n<1M
ClinVar Variant Effect Prediction Benchmark
Dataset Description
A curated subset of the NCBI ClinVar database (release: February 28, 2024). Each variant includes precomputed scores from Evo 2 and a set of baseline models used in the paper. Variants were filtered to retain only those with a ClinVar final review status of two gold stars or higher, ensuring higher-confidence clinical annotations supported by multiple submitters or expert panels.
Column Descriptions
Variant Metadata
| Column | Description |
|---|---|
variant_id |
Concatenation of the chromosome number and ClinVar's official variant ID. |
variant_type |
Type of genomic variant (e.g., SNV, deletion, insertion). |
chrom |
Chromosome number. |
chrom_refseq_acc |
RefSeq accession for the chromosome. |
start |
Genomic start position (1-based). |
stop |
Genomic end position (1-based). |
strand |
Strand orientation (+ or −). |
ref_allele |
Reference allele. |
alt_allele |
Alternate allele. |
transcript_id |
Transcript affected by the variant. |
Annotations
| Column | Description |
|---|---|
clinical_significance |
ClinVar-assigned clinical significance (e.g., pathogenic, benign, uncertain significance). |
clinsig |
Simplified clinical significance label used for model evaluation. (P/LP vs. B/LB) |
review_status |
ClinVar review status indicating the level of supporting evidence. |
gtf_feature |
GTF feature (CDS, 3'UTR, 5'UTR, or intergenic) encompassing the variant. |
splice_proximity |
Variant's proximity to the nearest transcript splice site. |
Model Scores
The remaining columns contain precomputed variant effect scores, one per model. These span genomic, RNA, and protein foundation models — including Evo 2 (7B and 40B), Evo, Nucleotide Transformer, CodonBERT, EnCodon, CaLM, ESM-2, ESM-1b, and RNA-FM as well as splice effect predictors (SpliceAI, Pangolin) and other baselines such as AlphaMissense, GPN-MSA, CADD, and phyloP conservation scores (100/241/447/470-way alignments).