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

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so the ClinVar-benign negatives overlap their training data.; Single-author bioRxiv preprint (v1, posted 2026-07-23), not peer reviewed; the analysis code is in the linked repository.; Scores are dbNSFP 5.3.1a rank scores; tool coverage differs, so each row has its own n and positives.; No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

• uses data: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels
• assessment: AlphaMissense on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: BayesDel_addAF on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: BayesDel_noAF on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: bStatistic on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: CADD_raw on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: ClinPred on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: DANN on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: DEOGEN2 on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: Eigen-PC-raw_coding on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: Eigen-raw_coding on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: ESM1b on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: fathmm-XF_coding on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: GERP_92_mammals on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: GERPpp_RS on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: gMVP on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: LIST-S2 on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: M-CAP on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MetaLR on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MetaRNN on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MetaSVM on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MisFit_D on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MisFit_S on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MPC on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MutationAssessor on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MutationTaster on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MutFormer on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MutPred2 on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MutScore on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: MVP on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: PHACTboost on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: phastCons100way_vertebrate on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: phastCons17way_primate on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: phastCons470way_mammalian on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: phyloP100way_vertebrate on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: phyloP17way_primate on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: phyloP470way_mammalian on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: Polyphen2_HDIV on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: Polyphen2_HVAR on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: popEVE on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: PrimateAI on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: PROVEAN on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: REVEL on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: SIFT on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: SIFT4G on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: VARITY_ER_LOO on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: VARITY_ER on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: VARITY_R_LOO on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: VARITY_R on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessment: VEST4 on CGC missense, tumour suppressors (loss of function) (Lee 2026)
• assessed by: Assess somatic small-variant oncogenicity