Dataset

COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)

COSMIC somatic missense mutations with frequency above 0.1% as positives and gnomAD common 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: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.325 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Configuration: GPN-MSA ablation '51 mammals' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.323 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Configuration: GPN-MSA ablation '51 vertebrates' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.347 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Configuration: GPN-MSA ablation '51 vertebrates' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.342 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Configuration: GPN-MSA ablation 'Default' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.355 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Configuration: GPN-MSA ablation 'Default' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.348 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Configuration: GPN-MSA ablation 'Include closest primates' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.219 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Configuration: GPN-MSA ablation 'Include closest primates' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.214 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Method: MSA frequency	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.27 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Method: MSA frequency	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.27 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Configuration: GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.34 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Configuration: GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.333 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Configuration: GPN-MSA ablation 'Don’t upweight conserved' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.309 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Configuration: GPN-MSA ablation 'Don’t upweight conserved' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.303 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Method: Combined phyloP and phastCons	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.141 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Method: Combined phyloP and phastCons	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.141 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Configuration: GPN-MSA ablation 'Train on 100% of genome' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.224 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Configuration: GPN-MSA ablation 'Train on 100% of genome' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.21 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Configuration: GPN-MSA ablation 'Train on 50% most conserved' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.257 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Configuration: GPN-MSA ablation 'Train on 50% most conserved' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.241 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 16' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.25 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Configuration: GPN-MSA ablation 'Window size = 16' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.246 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 256' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.376 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'
Configuration: GPN-MSA ablation 'Window size = 256' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.366 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 32' (Supplementary Table 4)	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.328 AUPRC (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 COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc 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 'COSMIC' / 'max'

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6 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 COSMIC missense mutations with frequency > 0.1% 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' (COSMIC, gnomAD) and 'Main VEP metrics' (COSMIC) 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
Source location Methods 'VEP data sources' (COSMIC, gnomAD) and 'Main VEP metrics' (COSMIC) 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' (COSMIC, gnomAD) and 'Main VEP metrics' (COSMIC) 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
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' (COSMIC, gnomAD) and 'Main VEP metrics' (COSMIC) 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
Version COSMIC Cosmic_MutantCensus v98 GRCh38 (frequency over whole-genome or whole-exome samples); gnomAD v3.1.2 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' (COSMIC, gnomAD) and 'Main VEP metrics' (COSMIC) 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
Description COSMIC somatic missense mutations with frequency above 0.1% as positives and gnomAD common 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' (COSMIC, gnomAD) and 'Main VEP metrics' (COSMIC) 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
Name COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper) 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' (COSMIC, gnomAD) and 'Main VEP metrics' (COSMIC) Version: bioRxiv v2, posted 2024-04-06 Retrieved: 2026-10-14T12:02:16Z	not individually reviewed No individual claim review recorded Audit details Field: `name` 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

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

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GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Original source · bioRxiv v2, posted 2024-04-06

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Technical metadata and extraction receipts

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

areas: dna-genomes
contexts: research
version: COSMIC Cosmic_MutantCensus v98 GRCh38 (frequency over whole-genome or whole-exome samples); gnomAD v3.1.2
split: Whole labelled set; no training on labels (zero-shot scores)
population: COSMIC missense mutations with frequency > 0.1% versus gnomAD missense variants with MAF > 5%
source locator: Methods 'VEP data sources' (COSMIC, gnomAD) and 'Main VEP metrics' (COSMIC)
missing metadata: denominator: reason: unreported; note: Variant counts are not printed in the text or Supplementary Table 4

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