Dataset

ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)

ClinVar 'Pathogenic' missense variants as positives and gnomAD common (MAF > 5%) missense variants as controls.

Evaluation results

17 evaluations · 34 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GPN-MSA ablation '51 mammals' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.965 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 51 mammals on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row '51 mammals', column 'ClinVar' / 'max'
Configuration: GPN-MSA ablation '51 mammals' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.964 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 51 mammals on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row '51 mammals', column 'ClinVar' / 'mean'
Configuration: GPN-MSA ablation '51 vertebrates' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.967 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 51 vertebrates on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row '51 vertebrates', column 'ClinVar' / 'max'
Configuration: GPN-MSA ablation '51 vertebrates' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.967 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 51 vertebrates on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row '51 vertebrates', column 'ClinVar' / 'mean'
Configuration: GPN-MSA ablation 'Default' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.969 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Default on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Default', column 'ClinVar' / 'max'
Configuration: GPN-MSA ablation 'Default' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.969 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Default on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Default', column 'ClinVar' / 'mean'
Configuration: GPN-MSA ablation 'Include closest primates' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.956 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Include closest primates on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Include closest primates', column 'ClinVar' / 'max'
Configuration: GPN-MSA ablation 'Include closest primates' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.954 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Include closest primates on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Include closest primates', column 'ClinVar' / 'mean'
Method: MSA frequency	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.95 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSA frequency (no neural net) on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'MSA frequency (no neural net)', column 'ClinVar' / 'max'
Method: MSA frequency	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.95 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSA frequency (no neural net) on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'MSA frequency (no neural net)', column 'ClinVar' / 'mean'
Configuration: GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.967 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Don’t replace non-conserved on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Don’t replace non-conserved', column 'ClinVar' / 'max'
Configuration: GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.966 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Don’t replace non-conserved on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Don’t replace non-conserved', column 'ClinVar' / 'mean'
Configuration: GPN-MSA ablation 'Don’t upweight conserved' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.967 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Don’t upweight conserved on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Don’t upweight conserved', column 'ClinVar' / 'max'
Configuration: GPN-MSA ablation 'Don’t upweight conserved' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.967 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Don’t upweight conserved on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Don’t upweight conserved', column 'ClinVar' / 'mean'
Method: Combined phyloP and phastCons	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.928 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Combined phyloP and phastCons on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Combined phyloP and phastCons', column 'ClinVar' / 'max'
Method: Combined phyloP and phastCons	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.928 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Combined phyloP and phastCons on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Combined phyloP and phastCons', column 'ClinVar' / 'mean'
Configuration: GPN-MSA ablation 'Train on 100% of genome' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.961 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Train on 100% of genome on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Train on 100% of genome', column 'ClinVar' / 'max'
Configuration: GPN-MSA ablation 'Train on 100% of genome' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.96 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Train on 100% of genome on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Train on 100% of genome', column 'ClinVar' / 'mean'
Configuration: GPN-MSA ablation 'Train on 50% most conserved' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.963 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Train on 50% most conserved on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Train on 50% most conserved', column 'ClinVar' / 'max'
Configuration: GPN-MSA ablation 'Train on 50% most conserved' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.963 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Train on 50% most conserved on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Train on 50% most conserved', column 'ClinVar' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 16' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.965 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Window size = 16 on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Window size = 16', column 'ClinVar' / 'max'
Configuration: GPN-MSA ablation 'Window size = 16' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.964 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Window size = 16 on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Window size = 16', column 'ClinVar' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 256' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.969 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Window size = 256 on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Window size = 256', column 'ClinVar' / 'max'
Configuration: GPN-MSA ablation 'Window size = 256' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.969 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Window size = 256 on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Window size = 256', column 'ClinVar' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 32' (Supplementary Table 4)	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.967 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Window size = 32 on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Window size = 32', column 'ClinVar' / 'max'

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12 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Population ClinVar 'Pathogenic' missense versus gnomAD missense variants with MAF > 5% Context-only references	GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Original source ↗ Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v2, posted 2024-04-06 Retrieved: 2026-10-14T12:02:16Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `10411077df1ae59614f9a9a9f85384103d54127ba67a9b3c469a4a2d6c33cee4` Hash scope: SHA-256 of the PDF bytes as downloaded 2026-10-14T12:02:16Z. bioRxiv rewrites the XMP dates and document IDs, the Info ModDate and the trailer /ID on download, so a re-download does not reproduce the hash; the review found a fresh copy of the same length differing only in those 51 bytes, with an identical pdftotext -layout text layer. Inspected artifact
Population ClinVar 'Pathogenic' missense versus gnomAD missense variants with MAF > 5% Context-only references	songlab-cal/gpn docs/models/gpn-msa.md at commit dc5fd287 Original source ↗ Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: git commit dc5fd287599f2955a79d010bca0e0f7f8178c67e (main, committed 2026-09-26) Retrieved: 2026-10-14T12:06:06Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `8076d5e5ced9447904acc6fce3352030299e8701220f738b047fcefd0a1edaee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Context-only references	GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Original source ↗ Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v2, posted 2024-04-06 Retrieved: 2026-10-14T12:02:16Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `10411077df1ae59614f9a9a9f85384103d54127ba67a9b3c469a4a2d6c33cee4` Hash scope: SHA-256 of the PDF bytes as downloaded 2026-10-14T12:02:16Z. bioRxiv rewrites the XMP dates and document IDs, the Info ModDate and the trailer /ID on download, so a re-download does not reproduce the hash; the review found a fresh copy of the same length differing only in those 51 bytes, with an identical pdftotext -layout text layer. Inspected artifact
Source location Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Context-only references	songlab-cal/gpn docs/models/gpn-msa.md at commit dc5fd287 Original source ↗ Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: git commit dc5fd287599f2955a79d010bca0e0f7f8178c67e (main, committed 2026-09-26) Retrieved: 2026-10-14T12:06:06Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `8076d5e5ced9447904acc6fce3352030299e8701220f738b047fcefd0a1edaee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split Whole labelled set; no training on labels (zero-shot scores) Context-only references	GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Original source ↗ Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v2, posted 2024-04-06 Retrieved: 2026-10-14T12:02:16Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `10411077df1ae59614f9a9a9f85384103d54127ba67a9b3c469a4a2d6c33cee4` Hash scope: SHA-256 of the PDF bytes as downloaded 2026-10-14T12:02:16Z. bioRxiv rewrites the XMP dates and document IDs, the Info ModDate and the trailer /ID on download, so a re-download does not reproduce the hash; the review found a fresh copy of the same length differing only in those 51 bytes, with an identical pdftotext -layout text layer. Inspected artifact
Split Whole labelled set; no training on labels (zero-shot scores) Context-only references	songlab-cal/gpn docs/models/gpn-msa.md at commit dc5fd287 Original source ↗ Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: git commit dc5fd287599f2955a79d010bca0e0f7f8178c67e (main, committed 2026-09-26) Retrieved: 2026-10-14T12:06:06Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `8076d5e5ced9447904acc6fce3352030299e8701220f738b047fcefd0a1edaee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Version ClinVar release 20230730; gnomAD v3.1.2 (allele number at least 25,000 and official QC flags) Context-only references	GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Original source ↗ Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v2, posted 2024-04-06 Retrieved: 2026-10-14T12:02:16Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `10411077df1ae59614f9a9a9f85384103d54127ba67a9b3c469a4a2d6c33cee4` Hash scope: SHA-256 of the PDF bytes as downloaded 2026-10-14T12:02:16Z. bioRxiv rewrites the XMP dates and document IDs, the Info ModDate and the trailer /ID on download, so a re-download does not reproduce the hash; the review found a fresh copy of the same length differing only in those 51 bytes, with an identical pdftotext -layout text layer. Inspected artifact
Version ClinVar release 20230730; gnomAD v3.1.2 (allele number at least 25,000 and official QC flags) Context-only references	songlab-cal/gpn docs/models/gpn-msa.md at commit dc5fd287 Original source ↗ Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: git commit dc5fd287599f2955a79d010bca0e0f7f8178c67e (main, committed 2026-09-26) Retrieved: 2026-10-14T12:06:06Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `8076d5e5ced9447904acc6fce3352030299e8701220f738b047fcefd0a1edaee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description ClinVar 'Pathogenic' missense variants as positives and gnomAD common (MAF > 5%) missense variants as controls. Context-only references	GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Original source ↗ Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v2, posted 2024-04-06 Retrieved: 2026-10-14T12:02:16Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `10411077df1ae59614f9a9a9f85384103d54127ba67a9b3c469a4a2d6c33cee4` Hash scope: SHA-256 of the PDF bytes as downloaded 2026-10-14T12:02:16Z. bioRxiv rewrites the XMP dates and document IDs, the Info ModDate and the trailer /ID on download, so a re-download does not reproduce the hash; the review found a fresh copy of the same length differing only in those 51 bytes, with an identical pdftotext -layout text layer. Inspected artifact
Description ClinVar 'Pathogenic' missense variants as positives and gnomAD common (MAF > 5%) missense variants as controls. Context-only references	songlab-cal/gpn docs/models/gpn-msa.md at commit dc5fd287 Original source ↗ Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: git commit dc5fd287599f2955a79d010bca0e0f7f8178c67e (main, committed 2026-09-26) Retrieved: 2026-10-14T12:06:06Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `8076d5e5ced9447904acc6fce3352030299e8701220f738b047fcefd0a1edaee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 source records 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
songlab-cal/gpn docs/models/gpn-msa.md at commit dc5fd287 · Original source · git commit dc5fd287599f2955a79d010bca0e0f7f8178c67e (main, committed 2026-09-26)

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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-gpnmsa-data-clinvar-vs-gnomad-common-missense

areas: dna-genomes
contexts: research
version: ClinVar release 20230730; gnomAD v3.1.2 (allele number at least 25,000 and official QC flags)
split: Whole labelled set; no training on labels (zero-shot scores)
population: ClinVar 'Pathogenic' missense versus gnomAD missense variants with MAF > 5%
source locator: Methods 'VEP data sources' (ClinVar, gnomAD) and 'Main VEP metrics' (ClinVar)
missing metadata: denominator: reason: unreported; note: Variant counts are not printed in the text or Supplementary Table 4

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