Protocol

CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv)

AUROC and average precision (labelled AUPRC) of 49 predictor and conservation scores on tumour suppressors (loss of function).

49 evaluations · 98 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

49 recorded evaluations, 98 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

49 evaluations · 98 results. Different protocols are not a single leaderboard.

Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) · Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels

Sorted by AUROC (CGC missense, tumour suppressors (loss of function)) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	AUROC (CGC missense, tumour suppressors (loss of function))	Average precision (CGC missense, tumour suppressors (loss of function))
gMVP rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.913 (best in column)	0.731
AlphaMissense rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.9	0.749 (best in column)
ClinPred rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.898	0.717
MutScore rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.898	0.72
MutationTaster rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.897	0.616
MutPred2 rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.896	0.661
VARITY_R rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.894	0.69
CADD_raw rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.894	0.646
VARITY_R_LOO rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.893	0.683
BayesDel_addAF rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.892	0.684
MetaRNN rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.889	0.715
PHACTboost rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.889	0.707
VARITY_ER rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.886	0.658
VARITY_ER_LOO rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.886	0.656
VEST4 rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.885	0.626
MisFit_D rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.883	0.662
Eigen-raw_coding rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.874	0.606
MPC rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.873	0.626
PrimateAI rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.872	0.505
BayesDel_noAF rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.867	0.63
Eigen-PC-raw_coding rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.865	0.574
REVEL rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.859	0.618
PROVEAN rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.859	0.548
ESM1b rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.858	0.594
fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.857	0.476
Polyphen2_HVAR rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.852	0.482
SIFT4G rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.847	0.471
Polyphen2_HDIV rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.847	0.409
MisFit_S rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.846	0.635
popEVE rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.842	0.614
DEOGEN2 rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.841	0.596
LIST-S2 rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.832	0.536
MutationAssessor rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.824	0.535
DANN rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.823	0.378
phyloP100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.818	0.422
SIFT rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.817	0.383
MVP rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.803	0.502
M-CAP rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.803	0.478
MetaSVM rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.794	0.5
MetaLR rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.788	0.522
phyloP470way_mammalian rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.786	0.31
GERPpp_RS rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.757	0.253
GERP_92_mammals rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.742	0.198
phastCons100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.72	0.206
phastCons470way_mammalian rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.693	0.19
phastCons17way_primate rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.667	0.204
MutFormer rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.655	0.286
phyloP17way_primate rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.61	0.152
bStatistic rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	0.384	0.0951

All 98 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaMissense rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.749 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'AlphaMissense', group 'TSG', column 'AUPRC'
Configuration: AlphaMissense rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.9 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'AlphaMissense', group 'TSG', column 'AUROC'
Configuration: BayesDel_addAF rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.684 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel_addAF on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'BayesDel_addAF', group 'TSG', column 'AUPRC'
Configuration: BayesDel_addAF rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.892 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel_addAF on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'BayesDel_addAF', group 'TSG', column 'AUROC'
Configuration: BayesDel_noAF rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.63 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel_noAF on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'BayesDel_noAF', group 'TSG', column 'AUPRC'
Configuration: BayesDel_noAF rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.867 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel_noAF on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'BayesDel_noAF', group 'TSG', column 'AUROC'
Configuration: bStatistic rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.0951 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source bStatistic on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'bStatistic', group 'TSG', column 'AUPRC'
Configuration: bStatistic rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.384 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source bStatistic on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'bStatistic', group 'TSG', column 'AUROC'
Configuration: CADD_raw rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.646 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD_raw on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'CADD_raw', group 'TSG', column 'AUPRC'
Configuration: CADD_raw rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.894 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD_raw on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'CADD_raw', group 'TSG', column 'AUROC'
Configuration: ClinPred rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.717 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ClinPred on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'ClinPred', group 'TSG', column 'AUPRC'
Configuration: ClinPred rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.898 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ClinPred on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'ClinPred', group 'TSG', column 'AUROC'
Configuration: DANN rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.378 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DANN on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'DANN', group 'TSG', column 'AUPRC'
Configuration: DANN rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.823 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DANN on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'DANN', group 'TSG', column 'AUROC'
Configuration: DEOGEN2 rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.596 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DEOGEN2 on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'DEOGEN2', group 'TSG', column 'AUPRC'
Configuration: DEOGEN2 rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.841 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DEOGEN2 on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'DEOGEN2', group 'TSG', column 'AUROC'
Configuration: Eigen-PC-raw_coding rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.574 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Eigen-PC-raw_coding on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'Eigen-PC-raw_coding', group 'TSG', column 'AUPRC'
Configuration: Eigen-PC-raw_coding rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.865 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Eigen-PC-raw_coding on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'Eigen-PC-raw_coding', group 'TSG', column 'AUROC'
Configuration: Eigen-raw_coding rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.606 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Eigen-raw_coding on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'Eigen-raw_coding', group 'TSG', column 'AUPRC'
Configuration: Eigen-raw_coding rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.874 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Eigen-raw_coding on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'Eigen-raw_coding', group 'TSG', column 'AUROC'
Configuration: ESM1b rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.594 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM1b on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'ESM1b', group 'TSG', column 'AUPRC'
Configuration: ESM1b rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.858 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM1b on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'ESM1b', group 'TSG', column 'AUROC'
Configuration: fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.476 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source fathmm-XF_coding on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'fathmm-XF_coding', group 'TSG', column 'AUPRC'
Configuration: fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.857 AUROC (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source fathmm-XF_coding on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'fathmm-XF_coding', group 'TSG', column 'AUROC'
Configuration: GERP_92_mammals rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.198 Average precision (CGC missense, tumour suppressors (loss of function)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GERP_92_mammals on CGC missense, tumour suppressors (loss of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-tsg Aggregation: Not reported 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) · OncoCal tables/tool_performance.tsv at commit 40b7770f2a76, row tool 'GERP_92_mammals', group 'TSG', column 'AUPRC'

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An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers · Original source · bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page
OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) · Original source · commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11)

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Stable ID: somatic-oncogenicity-20261009-protocol-lee2026-tsg

areas: dna-genomes
contexts: clinical_research
protocol: Each dbNSFP 5.3.1a rank score is used directly to rank labelled variants; AUROC and average precision (labelled AUPRC) are computed per tool on the variants it scores, for all genes and by gene role.
version: tables/tool_performance.tsv rows with group 'TSG'
metric: auroc
limitations: Negatives are ClinVar benign or likely benign and gnomAD common variants, that is germline-benign labels; the use case does not accept these as automatic somatic negatives.; Many supervised tools were trained on ClinVar labels, so the ClinVar-benign negatives overlap their training data.; Single-author bioRxiv preprint (v1, posted 2026-07-23), not peer reviewed; the analysis code is in the linked repository.; Scores are dbNSFP 5.3.1a rank scores; tool coverage differs, so each row has its own n and positives.; No uncertainty is printed in this table. The preprint Results give VARITY_R 0.874 and AlphaMissense 0.868, matching the table; the OncoCal section gives 0.871 and 0.870, probably on the unique protein-level set used to train OncoCal.; Gene role uses CGC gene-level roles where variant-level CIViC mechanism is missing, so some variants may be assigned the wrong mechanism.; The table cannot be regenerated from the repository alone: its script (src/evaluation/part_b.py) needs dbNSFP 5.3.1a and COSMIC v104, which are not redistributed. It was added in the first commit (b17e658d6b) and is unchanged at the pinned commit, whose message credits an AI coding assistant but does not touch the table or its script.
source locator: OncoCal tables/tool_performance.tsv at 40b7770f2a76, group 'TSG'; preprint S1 Table and Fig 1A

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