Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
Rank score of each VEP from per-protein pairwise AUROC comparisons on 819 proteins (Table S8 rank_score).
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
85 recorded evaluations, 85 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
85 evaluations · 85 results. Different protocols are not a single leaderboard.
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)
Sorted by 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) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
All 85 result rows with coverage, uncertainty and sources
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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') |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- 3Cnet: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- AlphaMissense: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- AlphScore: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- BayesDel: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- BayesDel_noAF: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- BLOSUM62: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- CADD_1.7: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- CADD: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- CAPICE: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- ClinPred: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- CONDEL: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- COSMIS: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- External evaluations
- 85
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
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This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
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Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Original source · PMC12016141 (published 2025-04-22; Genome Biol 26:104)
- Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) · Original source · 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141
Technical metadata and extraction receipts
Stable ID: vep-lit-20261014-protocol-livesey2025-clinical-auroc
- areas
- dna-genomes; proteins-complexes
- contexts
- clinical_research
- scope note
- For each protein with at least 10 ClinVar pathogenic or likely pathogenic and 10 gnomAD v4.1 missense variants, the AUROC of each pair of VEPs is compared on variants scored by both; the higher AUROC wins. Win rates across proteins are averaged over all other VEPs. No training variants were removed, so clinical-trained VEPs can benefit from circularity.
- task
- Clinical variant classification ranking
- metric
- pairwise-win-rate
- metric direction
- higher
- unit
- percent
- metric qualifier
- 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
- metric implementation
- sklearn.metrics.roc_auc_score (sklearn 0.18.1); scores of VEPs where low means pathogenic are inverted by subtracting from 1; the higher AUROC on shared variants earns the point
- aggregation
- Win rate of each VEP pair across proteins (wins divided by times the pair was tested), averaged over all other VEPs (Methods, 'Spearman's correlation and rank score')
- version
- Livesey and Marsh 2025, Supplementary Material 2 Table S8
- publication status
- peer_reviewed
- source locator
- Methods 'Spearman's correlation and rank score' and 'AUROC and AUPRC'; Supplementary Material 2 Legends (Table S8)
- limitations
- A rank score is relative to the other VEPs in the same table; values from different tables or editions are not comparable.; Per-pair, per-protein correlations and AUROCs behind the win rates are not printed; they are in the figshare deposit, which was not retrieved.; Clinical-trained VEPs were not filtered for training overlap; the authors attribute most of their advantage here to circularity (Results, Fig. 4).; Figure 3 error bars are the standard error across comparisons; they are not printed.; The text says 83 VEPs were tested (46 clinical-trained, 31 population-free, 6 population-tuned; Results and Fig. 3 legend) and that CPT-1 outperforms 38 of 48 clinical-trained VEPs (Discussion); Table S8 has 85 rows, including 'CADD' and 'COSMIS', which have no Table S2 row. The rank scores are those printed against the 85 columns of Table S8; the discrepancy is not explained.
- review
- reviewer: claude; reviewer note: Claude review agent; no human review claimed. Independent Claude (Opus 5.5) review agent, separate from the extraction agent that built this batch. Automated review only. Transcription, not reproduction.; reviewed at: 2026-10-14T15:30:00Z; artifact sha256: 1735ee461ef192d9de67c914e9ad73d72d8aa255ea0e3479eb68cd8631d99fa2; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12016141/fullTextXML; method: ai-assisted-source-review; scope-review; method note: Descriptive fields, identity links and missing-metadata reasons checked against the cited sources.; note: Checked; see the dated review for rulings on identity and method type.
Related records
- part of: Livesey and Marsh variant effect predictor benchmark (2025 edition)
- uses data: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins)
- assessed by: Interpret BRCA1/BRCA2 germline variants
- assessed by: Use calibrated computational evidence for missense variants (PP3/BP4)
- assessed by: Rank rare-disease variants for review
- assessment: 3Cnet: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: AlphaMissense: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: AlphScore: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: BayesDel: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: BayesDel_noAF: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: BLOSUM62: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: CADD_1.7: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: CADD: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: CAPICE: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: ClinPred: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: CONDEL: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: COSMIS: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: CPT-1: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: DANN: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: DeepSAV: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: DeepSequence: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: DeMaSk: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: DEOGEN2: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: Eigen: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: Envision: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: ESCOTT: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: ESM-1b: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: ESM-1v: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: ESM2: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: EVE: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: EVmutation_epistatic: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: EVmutation_independent: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: FATHMM: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: fathmm-MKL: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: FathmmXF: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: fitCons: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: GEMME: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: GenoCanyon: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: GERP++: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: gMVP: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: Grantham: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: iGEMME: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: InMeRF: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: LASSIE: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: LIST-S2: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: LRT: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: M-CAP: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: Maverick_benign: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: MetaLR: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: MetaRNN: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: MetaSVM: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: MISTIC: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: MOIpred_benign: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: MPC: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: MutationAssessor: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: mutationTCN: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: MutFormer: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: MutPred: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: MutScore: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: MVP: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: mvPPT: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: PHACT: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: PHACTboost: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: phastCons: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: PhD-SNPg: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: phyloP: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: PonP2: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: popEVE: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: PrimateAI: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: ProtGPT2: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: PROVEAN: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: REVEL: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: Rhapsody: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: SaProt: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: sequence_unet: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: SIFT: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: SIFT4G: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: SIGMA: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: SiPhy: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: SNAP2: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: SNPred: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: SPRI: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: SuSPect: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: Tranception: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: UNEECON: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: VARITY_ER: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: VARITY_R: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: VESPA: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: VESPAl: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- assessment: VEST4: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense