AlphaMissense rank score, dbNSFP 5.3.1a (Lee 2026)
AlphaMissense rank score, dbNSFP 5.3.1a: dbNSFP 5.3.1a rank score (GRCh38).
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
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)) |
|---|---|---|---|---|---|---|---|
| AlphaMissense rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation | CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv) | 0.868 | Not reported | Not reported | 0.75 | Not reported | Not reported |
| AlphaMissense rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation | CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv) | Not reported | 0.885 | Not reported | Not reported | 0.804 | Not reported |
| AlphaMissense 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 | 0.9 | Not reported | Not reported | 0.749 |
All 6 result rows with coverage, uncertainty and sources
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Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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How it works, versions and access
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Evidence
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Evidence table
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Sources and history
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)
Technical metadata and extraction receipts
Stable ID: somatic-oncogenicity-20261009-config-lee2026-alphamissense
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- supervised_machine_learning
- reported name
- AlphaMissense
- 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
- AlphaMissense as scored in the cited benchmark.