Dataset

Livesey and Marsh 2025 human DMS benchmark set (36 proteins)

One deep mutational scanning score set per protein for 36 human proteins, with variants present in ClinVar or gnomAD removed.

Evaluation results

485 evaluations · 582 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: 3Cnet (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	7.05% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV96)	Independent external evaluation · Source checked Methods, coverage and source 3Cnet: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU96 (row '3Cnet', column 'rank_score')
Configuration: 3Cnet (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	0% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3Cnet: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW96 (row '3Cnet', column 'top_5_winrate')
Configuration: AlphaMissense (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	90.7% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV3)	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU3 (row 'AlphaMissense', column 'rank_score')
Configuration: AlphaMissense (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	65.3% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW3 (row 'AlphaMissense', column 'top_5_winrate')
Configuration: AlphScore (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	33.5% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV76)	Independent external evaluation · Source checked Methods, coverage and source AlphScore: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU76 (row 'AlphScore', column 'rank_score')
Configuration: AlphScore (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	11% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphScore: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW76 (row 'AlphScore', column 'top_5_winrate')
Configuration: BayesDel_noAF (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	57.1% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV39)	Independent external evaluation · Source checked Methods, coverage and source BayesDel_noAF: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU39 (row 'BayesDel_noAF', column 'rank_score')
Configuration: BayesDel_noAF (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	6% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel_noAF: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW39 (row 'BayesDel_noAF', column 'top_5_winrate')
Configuration: BayesDel (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	56.9% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV40)	Independent external evaluation · Source checked Methods, coverage and source BayesDel: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU40 (row 'BayesDel', column 'rank_score')
Configuration: BayesDel (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	5.44% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW40 (row 'BayesDel', column 'top_5_winrate')
Configuration: BLOSUM62 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	14.9% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV87)	Independent external evaluation · Source checked Methods, coverage and source BLOSUM62: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU87 (row 'BLOSUM62', column 'rank_score')
Configuration: BLOSUM62 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	1.11% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BLOSUM62: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW87 (row 'BLOSUM62', column 'top_5_winrate')
Configuration: CADD_1.6 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	35% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV75)	Independent external evaluation · Source checked Methods, coverage and source CADD_1.6: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU75 (row 'CADD_1.6', column 'rank_score')
Configuration: CADD_1.6 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	1.22% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD_1.6: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW75 (row 'CADD_1.6', column 'top_5_winrate')
Configuration: CADD_1.7 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	40.3% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV70)	Independent external evaluation · Source checked Methods, coverage and source CADD_1.7: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU70 (row 'CADD_1.7', column 'rank_score')
Configuration: CADD_1.7 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	2.89% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD_1.7: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW70 (row 'CADD_1.7', column 'top_5_winrate')
Configuration: CAPICE (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	29.4% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV77)	Independent external evaluation · Source checked Methods, coverage and source CAPICE: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU77 (row 'CAPICE', column 'rank_score')
Configuration: CAPICE (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	3.69% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CAPICE: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW77 (row 'CAPICE', column 'top_5_winrate')
Configuration: CARP (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	76.1% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 28/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV17)	Independent external evaluation · Source checked Methods, coverage and source CARP: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU17 (row 'CARP', column 'rank_score')
Configuration: CARP (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	20% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CARP: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW17 (row 'CARP', column 'top_5_winrate')
Configuration: ClinPred (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	63.2% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV32)	Independent external evaluation · Source checked Methods, coverage and source ClinPred: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU32 (row 'ClinPred', column 'rank_score')
Configuration: ClinPred (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	4.36% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ClinPred: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW32 (row 'ClinPred', column 'top_5_winrate')
Configuration: CONDEL (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	47.5% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV57)	Independent external evaluation · Source checked Methods, coverage and source CONDEL: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU57 (row 'CONDEL', column 'rank_score')
Configuration: CONDEL (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	9.76% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONDEL: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW57 (row 'CONDEL', column 'top_5_winrate')
Configuration: CPT-1 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	92.8% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 29/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV2)	Independent external evaluation · Source checked Methods, coverage and source CPT-1: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU2 (row 'CPT-1', column 'rank_score')

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

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Verified: Not verified

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Verified: Not verified

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18 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
Access DMS and VEP predictions deposited at figshare doi:10.6084/m9.figshare.28295198 (Data availability); not retrieved in this pass. Context-only references	Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Original source ↗ Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) Retrieved: 2026-10-14T13:36:01Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.access` Source artifact SHA-256: `1735ee461ef192d9de67c914e9ad73d72d8aa255ea0e3479eb68cd8631d99fa2` Hash scope: Hash scope not separately documented; inspect source record
Access DMS and VEP predictions deposited at figshare doi:10.6084/m9.figshare.28295198 (Data availability); not retrieved in this pass. Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.access` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Assay Mixed: growth, complementation, binding, abundance (VAMP-seq), reporter and enzyme-activity assays, classed by the authors as direct or indirect (Table S1). Context-only references	Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Original source ↗ Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) Retrieved: 2026-10-14T13:36:01Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `1735ee461ef192d9de67c914e9ad73d72d8aa255ea0e3479eb68cd8631d99fa2` Hash scope: Hash scope not separately documented; inspect source record
Assay Mixed: growth, complementation, binding, abundance (VAMP-seq), reporter and enzyme-activity assays, classed by the authors as direct or indirect (Table S1). Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Population 36 human proteins, 207,460 single amino acid variants (Results). Per protein, the score set with the highest median Spearman correlation with all VEPs was chosen; datasets with fewer than 1000 scored substitutions after removing ClinVar and gnomAD variants, antibody-binding assays, the ACE2 to SARS-CoV-2 binding assay and datasets without methodological details were excluded. GCH1 is an unpublished dataset used with the authors' permission. Context-only references	Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Original source ↗ Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) Retrieved: 2026-10-14T13:36:01Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `1735ee461ef192d9de67c914e9ad73d72d8aa255ea0e3479eb68cd8631d99fa2` Hash scope: Hash scope not separately documented; inspect source record
Population 36 human proteins, 207,460 single amino acid variants (Results). Per protein, the score set with the highest median Spearman correlation with all VEPs was chosen; datasets with fewer than 1000 scored substitutions after removing ClinVar and gnomAD variants, antibody-binding assays, the ACE2 to SARS-CoV-2 binding assay and datasets without methodological details were excluded. GCH1 is an unpublished dataset used with the authors' permission. Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Source location Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Context-only references	Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Original source ↗ Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) Retrieved: 2026-10-14T13:36:01Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `1735ee461ef192d9de67c914e9ad73d72d8aa255ea0e3479eb68cd8631d99fa2` Hash scope: Hash scope not separately documented; inspect source record
Source location Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` 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) Original source ↗ Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) Retrieved: 2026-10-14T13:36:01Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.species` Source artifact SHA-256: `1735ee461ef192d9de67c914e9ad73d72d8aa255ea0e3479eb68cd8631d99fa2` Hash scope: Hash scope not separately documented; inspect source record
Species Homo sapiens Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.species` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record

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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

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Technical metadata and extraction receipts

Stable ID: vep-lit-20261014-dataset-livesey2025-dms-36

areas: proteins-complexes
contexts: research
population: 36 human proteins, 207,460 single amino acid variants (Results). Per protein, the score set with the highest median Spearman correlation with all VEPs was chosen; datasets with fewer than 1000 scored substitutions after removing ClinVar and gnomAD variants, antibody-binding assays, the ACE2 to SARS-CoV-2 binding assay and datasets without methodological details were excluded. GCH1 is an unpublished dataset used with the authors' permission.
variant count: 207460
split: No training split; zero-shot comparison of VEP scores with DMS scores. For Envision, CPT-1, DeMaSk, VARITY_R and VARITY_ER the DMS sets used to train them are excluded from their comparisons (Table S2).
assay: Mixed: growth, complementation, binding, abundance (VAMP-seq), reporter and enzyme-activity assays, classed by the authors as direct or indirect (Table S1).
species: Homo sapiens
access: DMS and VEP predictions deposited at figshare doi:10.6084/m9.figshare.28295198 (Data availability); not retrieved in this pass.
source locator: Results 'New DMS datasets and VEPs'; Methods 'DMS datasets'; Table 1; Supplementary Table S1; Data availability
missing metadata: version: reason: unreported; note: No dataset version beyond the paper; the figshare deposit was not retrieved.
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.

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: 3Cnet (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	7.05% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV96)	Independent external evaluation · Source checked Methods, coverage and source 3Cnet: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU96 (row '3Cnet', column 'rank_score')
Configuration: 3Cnet (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	0% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3Cnet: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW96 (row '3Cnet', column 'top_5_winrate')
Configuration: AlphaMissense (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	90.7% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV3)	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU3 (row 'AlphaMissense', column 'rank_score')
Configuration: AlphaMissense (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	65.3% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW3 (row 'AlphaMissense', column 'top_5_winrate')
Configuration: AlphScore (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	33.5% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV76)	Independent external evaluation · Source checked Methods, coverage and source AlphScore: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU76 (row 'AlphScore', column 'rank_score')
Configuration: AlphScore (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	11% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphScore: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW76 (row 'AlphScore', column 'top_5_winrate')
Configuration: BayesDel_noAF (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	57.1% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV39)	Independent external evaluation · Source checked Methods, coverage and source BayesDel_noAF: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU39 (row 'BayesDel_noAF', column 'rank_score')
Configuration: BayesDel_noAF (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	6% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel_noAF: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW39 (row 'BayesDel_noAF', column 'top_5_winrate')
Configuration: BayesDel (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	56.9% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV40)	Independent external evaluation · Source checked Methods, coverage and source BayesDel: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU40 (row 'BayesDel', column 'rank_score')
Configuration: BayesDel (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	5.44% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW40 (row 'BayesDel', column 'top_5_winrate')
Configuration: BLOSUM62 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	14.9% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV87)	Independent external evaluation · Source checked Methods, coverage and source BLOSUM62: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU87 (row 'BLOSUM62', column 'rank_score')
Configuration: BLOSUM62 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	1.11% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BLOSUM62: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW87 (row 'BLOSUM62', column 'top_5_winrate')
Configuration: CADD_1.6 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	35% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV75)	Independent external evaluation · Source checked Methods, coverage and source CADD_1.6: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU75 (row 'CADD_1.6', column 'rank_score')
Configuration: CADD_1.6 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	1.22% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD_1.6: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW75 (row 'CADD_1.6', column 'top_5_winrate')
Configuration: CADD_1.7 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	40.3% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV70)	Independent external evaluation · Source checked Methods, coverage and source CADD_1.7: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU70 (row 'CADD_1.7', column 'rank_score')
Configuration: CADD_1.7 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	2.89% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD_1.7: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW70 (row 'CADD_1.7', column 'top_5_winrate')
Configuration: CAPICE (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	29.4% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV77)	Independent external evaluation · Source checked Methods, coverage and source CAPICE: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU77 (row 'CAPICE', column 'rank_score')
Configuration: CAPICE (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	3.69% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CAPICE: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW77 (row 'CAPICE', column 'top_5_winrate')
Configuration: CARP (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	76.1% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 28/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV17)	Independent external evaluation · Source checked Methods, coverage and source CARP: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU17 (row 'CARP', column 'rank_score')
Configuration: CARP (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	20% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CARP: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW17 (row 'CARP', column 'top_5_winrate')
Configuration: ClinPred (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	63.2% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV32)	Independent external evaluation · Source checked Methods, coverage and source ClinPred: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU32 (row 'ClinPred', column 'rank_score')
Configuration: ClinPred (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	4.36% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ClinPred: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW32 (row 'ClinPred', column 'top_5_winrate')
Configuration: CONDEL (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	47.5% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV57)	Independent external evaluation · Source checked Methods, coverage and source CONDEL: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU57 (row 'CONDEL', column 'rank_score')
Configuration: CONDEL (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	9.76% Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CONDEL: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CW57 (row 'CONDEL', column 'top_5_winrate')
Configuration: CPT-1 (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	92.8% Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 29/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell CV2)	Independent external evaluation · Source checked Methods, coverage and source CPT-1: Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets 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 S3', cell CU2 (row 'CPT-1', column 'rank_score')