Dataset

gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)

gnomAD v3.1.2 singletons as the rare class and variants with minor allele frequency above 5% as the common class, all variant types, with rare variants subsampled to match the number of common variants per consequence.

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: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	43.4 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Configuration: GPN-MSA ablation '51 mammals' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	41.4 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Configuration: GPN-MSA ablation '51 vertebrates' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	46.8 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Configuration: GPN-MSA ablation '51 vertebrates' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	41.6 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Configuration: GPN-MSA ablation 'Default' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	43.1 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Configuration: GPN-MSA ablation 'Default' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	41.4 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Configuration: GPN-MSA ablation 'Include closest primates' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	26.7 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Configuration: GPN-MSA ablation 'Include closest primates' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	24.7 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Method: MSA frequency	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	15.1 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Method: MSA frequency	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	15.1 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Configuration: GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	45.2 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Configuration: GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	41.9 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Configuration: GPN-MSA ablation 'Don’t upweight conserved' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	40 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Configuration: GPN-MSA ablation 'Don’t upweight conserved' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	37.1 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Method: Combined phyloP and phastCons	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	13.9 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Method: Combined phyloP and phastCons	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	13.9 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Configuration: GPN-MSA ablation 'Train on 100% of genome' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	30.7 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Configuration: GPN-MSA ablation 'Train on 100% of genome' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	28 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Configuration: GPN-MSA ablation 'Train on 50% most conserved' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	35.3 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Configuration: GPN-MSA ablation 'Train on 50% most conserved' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	32.1 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 16' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	31.6 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Configuration: GPN-MSA ablation 'Window size = 16' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	29.2 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 256' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	43 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'max'
Configuration: GPN-MSA ablation 'Window size = 256' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	37.9 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 32' (Supplementary Table 4)	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	38.9 Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; 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 gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio 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 'gnomAD' / '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 gnomAD singletons versus gnomAD variants with MAF > 5%, all variant types; rare variants subsampled to the number of common variants per consequence 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' (gnomAD) and 'Additional VEP metrics' ('gnomAD (ablation set)'); Supplementary Table 4 caption 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' (gnomAD) and 'Additional VEP metrics' ('gnomAD (ablation set)'); Supplementary Table 4 caption 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' (gnomAD) and 'Additional VEP metrics' ('gnomAD (ablation set)'); Supplementary Table 4 caption 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' (gnomAD) and 'Additional VEP metrics' ('gnomAD (ablation set)'); Supplementary Table 4 caption 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 gnomAD v3.1.2 (allele number at least 25,000 and official quality-control 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' (gnomAD) and 'Additional VEP metrics' ('gnomAD (ablation set)'); Supplementary Table 4 caption 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 gnomAD v3.1.2 singletons as the rare class and variants with minor allele frequency above 5% as the common class, all variant types, with rare variants subsampled to match the number of common variants per consequence. 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' (gnomAD) and 'Additional VEP metrics' ('gnomAD (ablation set)'); Supplementary Table 4 caption 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 gnomAD rare (singletons) vs common variants, ablation set (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' (gnomAD) and 'Additional VEP metrics' ('gnomAD (ablation set)'); Supplementary Table 4 caption 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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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

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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-gpnmsa-data-gnomad-rare-vs-common-ablation-set

areas: dna-genomes
contexts: research
version: gnomAD v3.1.2 (allele number at least 25,000 and official quality-control flags)
split: Whole labelled set; no training on labels (zero-shot scores)
population: gnomAD singletons versus gnomAD variants with MAF > 5%, all variant types; rare variants subsampled to the number of common variants per consequence
source locator: Methods 'VEP data sources' (gnomAD) and 'Additional VEP metrics' ('gnomAD (ablation set)'); Supplementary Table 4 caption
missing metadata: denominator: reason: unreported; note: Variant counts of the ablation set are not printed

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