ClinVar pathogenic and likely pathogenic missense variants against 'putatively benign' gnomAD v4.1 missense variants, in proteins with at least 10 of each.
85 evaluations · 85 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: 3Cnet (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 20.8% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 434/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ76) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI76 (row '3Cnet', column 'rank_score') |
| Configuration: AlphaMissense (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 77.5% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 818/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ5) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI5 (row 'AlphaMissense', column 'rank_score') |
| Configuration: AlphScore (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 25.3% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 796/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ71) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI71 (row 'AlphScore', column 'rank_score') |
| Configuration: BayesDel_noAF (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 71.8% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 811/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ11) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI11 (row 'BayesDel_noAF', column 'rank_score') |
| Configuration: BayesDel (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 66.9% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 814/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ22) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI22 (row 'BayesDel', column 'rank_score') |
| Configuration: BLOSUM62 (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 11.3% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 819/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ83) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI83 (row 'BLOSUM62', column 'rank_score') |
| Configuration: CADD_1.7 (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 52.1% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 812/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ45) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI45 (row 'CADD_1.7', column 'rank_score') |
| Configuration: CADD (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 41.4% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 814/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ63) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI63 (row 'CADD', column 'rank_score') |
| Configuration: CAPICE (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 63.7% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 813/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ27) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI27 (row 'CAPICE', column 'rank_score') |
| Configuration: ClinPred (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 62.4% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 812/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ29) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI29 (row 'ClinPred', column 'rank_score') |
| Configuration: CONDEL (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 49.9% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 809/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ50) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI50 (row 'CONDEL', column 'rank_score') |
| Configuration: COSMIS (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 22.2% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 686/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ74) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI74 (row 'COSMIS', column 'rank_score') |
| Configuration: CPT-1 (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 71.7% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 783/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ12) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI12 (row 'CPT', column 'rank_score') |
| Configuration: DANN (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 27.9% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 814/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ70) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI70 (row 'DANN', column 'rank_score') |
| Configuration: DeepSAV (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 59.1% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 813/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ33) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI33 (row 'DeepSAV', column 'rank_score') |
| Configuration: DeepSequence (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 65.9% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 200/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ23) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI23 (row 'DeepSequence', column 'rank_score') |
| Configuration: DeMaSk (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 46.5% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 814/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ56) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI56 (row 'DeMaSk', column 'rank_score') |
| Configuration: DEOGEN2 (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 60.8% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 795/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ32) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI32 (row 'DEOGEN2', column 'rank_score') |
| Configuration: Eigen (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 54.6% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 738/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ41) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI41 (row 'Eigen', column 'rank_score') |
| Configuration: Envision (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 42.4% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 805/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ62) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI62 (row 'Envision', column 'rank_score') |
| Configuration: ESCOTT (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 66.9% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 755/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ21) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI21 (row 'ESCOTT', column 'rank_score') |
| Configuration: ESM-1b (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 54.3% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 814/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ42) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI42 (row 'ESM-1b', column 'rank_score') |
| Configuration: ESM-1v (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 61.4% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 814/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ31) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI31 (row 'ESM-1v', column 'rank_score') |
| Configuration: ESM2 (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 51.4% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 819/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ46) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI46 (row 'ESM2', column 'rank_score') |
| Configuration: EVE (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 69.6% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 738/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ15) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI15 (row 'EVE', column 'rank_score') |
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| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Access VEP predictions for these variants deposited at figshare doi:10.6084/m9.figshare.28295249 (Data availability); not retrieved in this pass. Context-only references | Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Methods 'ClinVar and gnomAD data'; Results 'Performance of VEPs on clinical variant classification'; Data availability Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Label semantics Positive: ClinVar pathogenic, likely pathogenic, pathogenic/likely pathogenic. Negative: gnomAD v4.1 missense variants, 'putatively benign', mostly rare; the authors note it will include some unclassified pathogenic variants, especially in recessive and incomplete-penetrance genes. Context-only references | Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Methods 'ClinVar and gnomAD data'; Results 'Performance of VEPs on clinical variant classification'; Data availability Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Population 819 human proteins with at least 10 pathogenic or likely pathogenic ClinVar missense variants (0-star and conflicting entries removed) and at least 10 gnomAD v4.1 missense variants that passed the genome or exome filters and were not classed pathogenic. Context-only references | Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Methods 'ClinVar and gnomAD data'; Results 'Performance of VEPs on clinical variant classification'; Data availability Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location Methods 'ClinVar and gnomAD data'; Results 'Performance of VEPs on clinical variant classification'; Data availability Context-only references | Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Methods 'ClinVar and gnomAD data'; Results 'Performance of VEPs on clinical variant classification'; Data availability Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Species Homo sapiens Context-only references | Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Methods 'ClinVar and gnomAD data'; Results 'Performance of VEPs on clinical variant classification'; Data availability Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Split No held-out split; no variants used in VEP training were removed, so clinical-trained VEPs can benefit from circularity (Results). Context-only references | Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Methods 'ClinVar and gnomAD data'; Results 'Performance of VEPs on clinical variant classification'; Data availability Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Version ClinVar obtained 06/08/2024 (date format not stated); gnomAD v4.1 Context-only references | Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Methods 'ClinVar and gnomAD data'; Results 'Performance of VEPs on clinical variant classification'; Data availability Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description ClinVar pathogenic and likely pathogenic missense variants against 'putatively benign' gnomAD v4.1 missense variants, in proteins with at least 10 of each. Context-only references | Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Methods 'ClinVar and gnomAD data'; Results 'Performance of VEPs on clinical variant classification'; Data availability Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Name Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) Context-only references | Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Methods 'ClinVar and gnomAD data'; Results 'Performance of VEPs on clinical variant classification'; Data availability Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: vep-lit-20261014-dataset-livesey2025-clinvar-gnomad-819