AlphScore
Random forest that scores missense variant pathogenicity from features of AlphaFold2 wild-type structures, such as solvent accessibility, residue network features and pLDDT, trained to separate common from singleton gnomAD v3.1 missense variants.
Results are recorded on linked configurations and versions of this method. Their settings and evaluations are kept separate below.
Results on linked records
This method has no results of its own in this release. One linked record has results. They are not assigned to the underlying method: each record keeps its own settings and evaluations, and its scores are on its own page.
- AlphScore (Livesey and Marsh 2025) Configuration · configuration · 6 evaluations · 7 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.
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How it works, versions and access
Strengths, limitations and unresolved questions
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) · Original source · 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141
- Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Original source · PMC12016141 (published 2025-04-22; Genome Biol 26:104)
Technical metadata and extraction receipts
Stable ID: vep-lit-20261014-method-alphscore
- areas
- dna-genomes; proteins-complexes
- contexts
- research; clinical_research
- method types
- supervised_machine_learning
- reported name
- AlphScore
- entity level
- method
- source locator
- Supplementary Material 2, Table S2 row 4 ('AlphScore')
- missing metadata
- version: reason: inapplicable; note: Family record; score versions are on configurations
- review
- reviewer: claude; reviewer note: Claude review agent; no human review claimed. Independent Claude (Opus 5.5) review agent, separate from the extraction agent that built this batch. Automated review only. Transcription, not reproduction.; reviewed at: 2026-10-14T15:30:00Z; artifact sha256: 1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70; retrieval url: https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-025-03575-w/MediaObjects/13059_2025_3575_MOESM2_ESM.xlsx; method: ai-assisted-source-review; scope-review; method note: Descriptive fields, identity links and missing-metadata reasons checked against the cited sources.; note: Checked; see the dated review for rulings on identity and method type.
- provenance note
- Livesey and Marsh 2025 class it as clinical-trained (trained on human variants with clinical labels, or using a predictor that was) and obtained its predictions from https://zenodo.org/records/6288139 (Table S2).
Related records
- configuration of: AlphScore (Livesey and Marsh 2025)