Configuration

phastCons100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026)

phastCons100way_vertebrate rank score, dbNSFP 5.3.1a: dbNSFP 5.3.1a rank score (GRCh38).

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Evaluations and results

3 evaluations · 6 results. Different protocols are not a single leaderboard.

Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels

Sorted by AUROC (CGC missense, all genes) (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	Protocol and dataset	AUROC (CGC missense, all genes)	AUROC (CGC missense, oncogenes (gain of function))	AUROC (CGC missense, tumour suppressors (loss of function))	Average precision (CGC missense, all genes)	Average precision (CGC missense, oncogenes (gain of function))	Average precision (CGC missense, tumour suppressors (loss of function))
phastCons100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv)	0.678	Not reported	Not reported	0.268	Not reported	Not reported
phastCons100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv)	Not reported	0.671	Not reported	Not reported	0.357	Not reported
phastCons100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation	CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv)	Not reported	Not reported	0.72	Not reported	Not reported	0.206

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: phastCons100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.268 Average precision (CGC missense, all genes) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phastCons100way_vertebrate on CGC missense, all genes (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-all 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 'phastCons100way_vertebrate', group 'all', column 'AUPRC'
Configuration: phastCons100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.678 AUROC (CGC missense, all genes) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phastCons100way_vertebrate on CGC missense, all genes (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-all 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 'phastCons100way_vertebrate', group 'all', column 'AUROC'
Configuration: phastCons100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.357 Average precision (CGC missense, oncogenes (gain 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 phastCons100way_vertebrate on CGC missense, oncogenes (gain of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-oncogene 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 'phastCons100way_vertebrate', group 'oncogene', column 'AUPRC'
Configuration: phastCons100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026)	Protocol: CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv) Dataset: Missense variants in 768 Cancer Gene Census genes with open oncogenicity labels	0.671 AUROC (CGC missense, oncogenes (gain 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 phastCons100way_vertebrate on CGC missense, oncogenes (gain of function) (Lee 2026) somatic-oncogenicity-20261009-protocol-lee2026-oncogene 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 'phastCons100way_vertebrate', group 'oncogene', column 'AUROC'
Configuration: phastCons100way_vertebrate 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	0.206 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 phastCons100way_vertebrate 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 'phastCons100way_vertebrate', group 'TSG', column 'AUPRC'
Configuration: phastCons100way_vertebrate 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	0.72 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 phastCons100way_vertebrate 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 'phastCons100way_vertebrate', group 'TSG', column 'AUROC'

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

2 source records and release history

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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Technical metadata and extraction receipts

Stable ID: somatic-oncogenicity-20261009-config-lee2026-phastcons100way-vertebrate

areas: dna-genomes
contexts: clinical_research
method types: specialist
reported name: phastCons100way_vertebrate
version: dbNSFP 5.3.1a rank score (GRCh38)
foundation model eligible: false
source locator: OncoCal tool_performance.tsv column 'tool'; preprint Methods 'Features'
provenance note: phastCons100way_vertebrate as scored in the cited benchmark.

Related records

configuration of: phastCons
system: phastCons100way_vertebrate on CGC missense, all genes (Lee 2026)
system: phastCons100way_vertebrate on CGC missense, oncogenes (gain of function) (Lee 2026)
system: phastCons100way_vertebrate on CGC missense, tumour suppressors (loss of function) (Lee 2026)

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