GPN-MSA variant effect prediction evaluation (Benegas et al.)
The authors' variant effect benchmarks in the GPN-MSA paper: ClinVar, COSMIC and OMIM against gnomAD common variants, gnomAD rare versus common enrichment, ProteinGym DMS and DepMap.
Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results on linked records
This benchmark has no results of its own in this release. 5 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.
- ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Protocol · part of this benchmark · 17 evaluations · 34 results
- COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Protocol · part of this benchmark · 17 evaluations · 34 results
- gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Protocol · part of this benchmark · 17 evaluations · 34 results
- OMIM pathogenic vs gnomAD common regulatory variants, AUPRC (GPN-MSA Supplementary Table 4) Protocol · part of this benchmark · 17 evaluations · 34 results
- ProteinGym DMS TADBP binary classification, AUROC (GPN-MSA paper) Protocol · part of this benchmark · 2 evaluations · 2 results
Methods and evaluation design
Procedure, tasks and evaluated configurations
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 10 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
- ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) · 0/2 roles measured
- COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) · 0/2 roles measured
- gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) · 0/2 roles measured
- OMIM pathogenic vs gnomAD common regulatory variants, AUPRC (GPN-MSA Supplementary Table 4) · 0/2 roles measured
- ProteinGym DMS TADBP binary classification, AUROC (GPN-MSA paper) · 0/2 roles measured
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
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Evidence table
Inspect claims, sources and review details
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Original source · bioRxiv v2, posted 2024-04-06
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-gpnmsa-benchmark-gpn-msa-vep
- areas
- dna-genomes
- contexts
- research
- entity level
- suite
- version
- bioRxiv v2 (2024-04-06)
- task
- Genome-wide variant effect (deleteriousness) prediction
- scope note
- Only Supplementary Table 4 (ablation study; ClinVar, COSMIC and OMIM columns) and the printed DMS TADBP AUROCs are extracted. The labelled datasets are published as songlab/clinvar, songlab/cosmic, songlab/omim and songlab/gnomad on Hugging Face (gpn-msa.md), not retrieved here.
- source locator
- Methods 'VEP data sources', 'Main VEP metrics' and 'Additional VEP metrics'
Related records
- part of: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4)
- part of: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4)
- part of: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4)
- part of: OMIM pathogenic vs gnomAD common regulatory variants, AUPRC (GPN-MSA Supplementary Table 4)
- part of: ProteinGym DMS TADBP binary classification, AUROC (GPN-MSA paper)