SIFT4G rank score, dbNSFP 5.3.1a (Lee 2026)
SIFT4G rank score, dbNSFP 5.3.1a: dbNSFP 5.3.1a rank score (GRCh38).
3 evaluations · 6 results5 open disagreements between studies involve its model
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)) |
|---|---|---|---|---|---|---|---|
| SIFT4G rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation | CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv) | 0.808 | Not reported | Not reported | 0.541 | Not reported | Not reported |
| SIFT4G rank score, dbNSFP 5.3.1a (Lee 2026)Evaluation | CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv) | Not reported | 0.786 | Not reported | Not reported | 0.572 | Not reported |
| SIFT4G 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 | 0.847 | Not reported | Not reported | 0.471 |
All 6 result rows with coverage, uncertainty and sources
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How it works, versions and access
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Evidence
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Evidence table
Inspect claims, sources and review details
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Facets: method types1 values
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations Chen et al. 2020 Table 1: SIFT uses a position-specific scoring matrix Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit detailsCorrect the method type from specialist to conventional_pipeline (use-case baseline review 2026-10-12, table 2). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: Field: Claim: metadata-correction-tags-20261012-a9b01b19c8ca3f15634d Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Facets: method types1 values
| An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Chen et al. 2020 Table 1: SIFT uses a position-specific scoring matrix Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page | conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit detailsCorrect the method type from specialist to conventional_pipeline (use-case baseline review 2026-10-12, table 2). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: Field: Claim: metadata-correction-tags-20261012-a9b01b19c8ca3f15634d Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. Extraction artifact SHA-256: |
Facets: method types1 values
| OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) Chen et al. 2020 Table 1: SIFT uses a position-specific scoring matrix Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11) | conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit detailsCorrect the method type from specialist to conventional_pipeline (use-case baseline review 2026-10-12, table 2). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: Field: Claim: metadata-correction-tags-20261012-a9b01b19c8ca3f15634d Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
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-sift4g
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- conventional_pipeline
- reported name
- SIFT4G
- 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
- SIFT4G as scored in the cited benchmark.