rewirebio.iobenchmarks
Contested result

CADD and FATHMM-XF: Comprehensive assessment of computational algorithms in predicting cancer driver mutations reverses the order

  • Low severity
  • Not yet reviewed
  • Ordering reversal
  • Different tasks across studies

Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks FATHMM-XF above CADD in 10 of 10 comparisons; other studies rank CADD above FATHMM-XF in 12 of 12.

An automatic lead, not a finding of error. The results below are shown as published, everywhere on the site, until a reviewer decides otherwise.

Which studies agree

2 papers rank CADD above FATHMM-XF in all 12 comparisons that are not ties (1 is a tie). Comprehensive assessment… ranks FATHMM-XF above CADD in all 10 of its comparisons.

Papers grouped by which system they rank higher: CADD or FATHMM-XFRank CADD higher: Livesey and Marsh 2025, An openly licensed benchmark…. Rank FATHMM-XF higher: Comprehensive assessment… (disagrees). Mixed: none.Rank CADD higherMixedRank FATHMM-XF higherLivesey and Marsh 2025Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)An openly licensedbenchmark…An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer driversComprehensive assessment…Comprehensive assessment of computational algorithms in predicting cancer driver mutations
  • Rank CADD higher (2): Livesey and Marsh 2025, An openly licensed benchmark…
  • Rank FATHMM-XF higher (1): Comprehensive assessment… (disagrees)
  • Mixed (0): none

Each paper sits where at least two thirds of its comparisons point; Mixed means neither model reaches two thirds. The larger, outlined dot is the paper that disagrees.

Comparisons in which each paper scores CADD or FATHMM-XF higherComprehensive assessment… (disagrees): CADD higher in 0, FATHMM-XF higher in 10, 0 ties. Livesey and Marsh 2025: CADD higher in 7, FATHMM-XF higher in 0, 0 ties. An openly licensed benchmark…: CADD higher in 5, FATHMM-XF higher in 0, 1 tie.Disagrees: Comprehensive assessment…Comprehensive assessment of computational algorithms in predicting cancer driver mutations10 FATHMM-XF higher10Livesey and Marsh 2025Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)7 CADD higher7An openly licensed benchmark…An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers5 CADD higher51 tie1
CADD higherTieFATHMM-XF higherNumbers are counts of comparisons; the outlined bar is the paper that disagrees.
Papers compared (3)
PaperRoleRanks CADD higherRanks FATHMM-XF higherTies
Comprehensive assessment of computational algorithms in predicting cancer driver mutations and 4 more records · DOIDisagrees0100
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) and 1 more record · DOIAgrees700
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers and 1 more record · DOIAgrees501
Comparisons in Comprehensive assessment… (10)
ProtocolDatasetMetricCADDFATHMM-XFHigher
OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)OncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)Accuracy (OncoKB benchmark (positive set not stated), median-score threshold), fraction0.640.65FATHMM-XF
OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)OncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)Negative predictive value (OncoKB benchmark (positive set not stated), median-score threshold), fraction0.640.65FATHMM-XF
OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)OncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)Precision (OncoKB benchmark (positive set not stated), median-score threshold), fraction0.640.65FATHMM-XF
OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)OncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)Recall (OncoKB benchmark (positive set not stated), median-score threshold), fraction0.640.65FATHMM-XF
OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)OncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)Specificity (OncoKB benchmark (positive set not stated), median-score threshold), fraction0.640.65FATHMM-XF
Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)Accuracy (cell viability drivers versus neutral, median-score threshold), fraction0.590.63FATHMM-XF
Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)Negative predictive value (cell viability drivers versus neutral, median-score threshold), fraction0.590.63FATHMM-XF
Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)Precision (cell viability drivers versus neutral, median-score threshold), fraction0.590.63FATHMM-XF
Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)Recall (cell viability drivers versus neutral, median-score threshold), fraction0.590.63FATHMM-XF
Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)Specificity (cell viability drivers versus neutral, median-score threshold), fraction0.590.63FATHMM-XF
Comparisons in Livesey and Marsh 2025 (7)
ProtocolDatasetMetricCADDFATHMM-XFHigher
Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missenseLivesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins)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), percent52.132CADD
Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS setsLivesey and Marsh 2025 human DMS benchmark set (36 proteins)Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, 36 human DMS sets), percent40.324.5CADD
Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS setsLivesey and Marsh 2025 human DMS benchmark set (36 proteins)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), percent2.891.83CADD
Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, direct assays onlyLivesey and Marsh 2025 human DMS benchmark set (36 proteins)Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, direct DMS assays only), percent3927.1CADD
Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, indirect assays onlyLivesey and Marsh 2025 human DMS benchmark set (36 proteins)Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, indirect DMS assays only), percent41.222.6CADD
Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions onlyLivesey and Marsh 2025 human DMS benchmark set (36 proteins)Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, SNV-accessible substitutions only), percent40.324.5CADD
Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions with gaps filledLivesey and Marsh 2025 human DMS benchmark set (36 proteins)Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS, SNV-accessible substitutions, missing predictions filled with the VEP's most benign score), percent4225.5CADD
Comparisons in An openly licensed benchmark… (6)
ProtocolDatasetMetricCADDFATHMM-XFHigher
CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv)Missense variants in 768 Cancer Gene Census genes with open oncogenicity labelsAUROC (CGC missense, all genes), unitless0.8260.813CADD
CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv)Missense variants in 768 Cancer Gene Census genes with open oncogenicity labelsAverage precision (CGC missense, all genes), unitless0.5960.568CADD
CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv)Missense variants in 768 Cancer Gene Census genes with open oncogenicity labelsAUROC (CGC missense, oncogenes (gain of function)), unitless0.8210.81CADD
CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv)Missense variants in 768 Cancer Gene Census genes with open oncogenicity labelsAverage precision (CGC missense, oncogenes (gain of function)), unitless0.6420.644Tie
CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv)Missense variants in 768 Cancer Gene Census genes with open oncogenicity labelsAUROC (CGC missense, tumour suppressors (loss of function)), unitless0.8940.857CADD
CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv)Missense variants in 768 Cancer Gene Census genes with open oncogenicity labelsAverage precision (CGC missense, tumour suppressors (loss of function)), unitless0.6460.476CADD

What disagrees

Other studies
rank CADD above FATHMM-XF in 12 of 12 comparisons
This study
ranks FATHMM-XF above CADD in 10 of 10 comparisons
Compared
CADD, FATHMM-XF
Study that disagrees
Comprehensive assessment of computational algorithms in predicting cancer driver mutations, Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB), Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability), Chen et al. 2020, Additional file 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability), Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB)
Other studies
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers, OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role), Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML), Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8)
Rule
Ordering reversal; different tasks across studies
Model identity
Matched across studies partly through links not yet reviewed

The compared numbers

Each value links to its result record and source. Compare values within one protocol; the rule compares rankings, not raw values across protocols.

In the study that disagrees (20)
StudyToolProtocol or benchmarkMetricValue
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB)CADD (Chen et al. 2020)OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)Accuracy (OncoKB benchmark (positive set not stated), median-score threshold)0.64
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB)CADD (Chen et al. 2020)OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)Negative predictive value (OncoKB benchmark (positive set not stated), median-score threshold)0.64
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB)CADD (Chen et al. 2020)OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)Precision (OncoKB benchmark (positive set not stated), median-score threshold)0.64
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB)CADD (Chen et al. 2020)OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)Recall (OncoKB benchmark (positive set not stated), median-score threshold)0.64
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB)CADD (Chen et al. 2020)OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)Specificity (OncoKB benchmark (positive set not stated), median-score threshold)0.64
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability)CADD (Chen et al. 2020)Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Accuracy (cell viability drivers versus neutral, median-score threshold)0.59
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability)CADD (Chen et al. 2020)Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Negative predictive value (cell viability drivers versus neutral, median-score threshold)0.59
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability)CADD (Chen et al. 2020)Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Precision (cell viability drivers versus neutral, median-score threshold)0.59
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability)CADD (Chen et al. 2020)Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Recall (cell viability drivers versus neutral, median-score threshold)0.59
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability)CADD (Chen et al. 2020)Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Specificity (cell viability drivers versus neutral, median-score threshold)0.59
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB)FATHMM-XF (Chen et al. 2020)OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)Accuracy (OncoKB benchmark (positive set not stated), median-score threshold)0.65
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB)FATHMM-XF (Chen et al. 2020)OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)Negative predictive value (OncoKB benchmark (positive set not stated), median-score threshold)0.65
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB)FATHMM-XF (Chen et al. 2020)OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)Precision (OncoKB benchmark (positive set not stated), median-score threshold)0.65
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB)FATHMM-XF (Chen et al. 2020)OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)Recall (OncoKB benchmark (positive set not stated), median-score threshold)0.65
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB)FATHMM-XF (Chen et al. 2020)OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)Specificity (OncoKB benchmark (positive set not stated), median-score threshold)0.65
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability)FATHMM-XF (Chen et al. 2020)Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Accuracy (cell viability drivers versus neutral, median-score threshold)0.63
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability)FATHMM-XF (Chen et al. 2020)Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Negative predictive value (cell viability drivers versus neutral, median-score threshold)0.63
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability)FATHMM-XF (Chen et al. 2020)Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Precision (cell viability drivers versus neutral, median-score threshold)0.63
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability)FATHMM-XF (Chen et al. 2020)Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Recall (cell viability drivers versus neutral, median-score threshold)0.63
Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability)FATHMM-XF (Chen et al. 2020)Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)Specificity (cell viability drivers versus neutral, median-score threshold)0.63
In the other studies (24)
StudyToolProtocol or benchmarkMetricValue
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role)CADD_raw rank score, dbNSFP 5.3.1a (Lee 2026)CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv)Average precision (CGC missense, all genes)0.596
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role)CADD_raw rank score, dbNSFP 5.3.1a (Lee 2026)CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv)AUROC (CGC missense, all genes)0.826
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role)CADD_raw rank score, dbNSFP 5.3.1a (Lee 2026)CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv)AUROC (CGC missense, oncogenes (gain of function))0.821
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role)CADD_raw rank score, dbNSFP 5.3.1a (Lee 2026)CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv)Average precision (CGC missense, tumour suppressors (loss of function))0.646
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role)CADD_raw rank score, dbNSFP 5.3.1a (Lee 2026)CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv)AUROC (CGC missense, tumour suppressors (loss of function))0.894
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role)fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026)CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv)Average precision (CGC missense, all genes)0.568
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role)fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026)CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv)AUROC (CGC missense, all genes)0.813
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role)fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026)CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv)AUROC (CGC missense, oncogenes (gain of function))0.81
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role)fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026)CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv)Average precision (CGC missense, tumour suppressors (loss of function))0.476
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role)fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026)CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv)AUROC (CGC missense, tumour suppressors (loss of function))0.857
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)CADD_1.7 (Livesey and Marsh 2025)Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missensePairwise 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)52.1
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)FathmmXF (Livesey and Marsh 2025)Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missensePairwise 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)32
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)CADD_1.7 (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS setsPairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, 36 human DMS sets)40.3
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)CADD_1.7 (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS setsPairwise 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)2.89
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)FathmmXF (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS setsPairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, 36 human DMS sets)24.5
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)FathmmXF (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS setsPairwise 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)1.83
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)CADD_1.7 (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, direct assays onlyPairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, direct DMS assays only)39
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)FathmmXF (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, direct assays onlyPairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, direct DMS assays only)27.1
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)CADD_1.7 (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, indirect assays onlyPairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, indirect DMS assays only)41.2
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)FathmmXF (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, indirect assays onlyPairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, indirect DMS assays only)22.6
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)CADD_1.7 (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions onlyPairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, SNV-accessible substitutions only)40.3
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)FathmmXF (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions onlyPairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, SNV-accessible substitutions only)24.5
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)CADD_1.7 (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions with gaps filledPairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS, SNV-accessible substitutions, missing predictions filled with the VEP's most benign score)42
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)FathmmXF (Livesey and Marsh 2025)Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions with gaps filledPairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS, SNV-accessible substitutions, missing predictions filled with the VEP's most benign score)25.5

Follow-up

Current state: Not yet reviewed.

No one has reviewed this finding yet.

How to help resolve this

If you know why these studies disagree, for example a different population, metric or preprocessing step, or you have a corrected value, tell us through the contribution form. A reviewer checks every submission against its source before anything changes, and the step is added to the follow-up above.

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