CADD (Livesey and Marsh 2025)
Configuration of CADD; no settings beyond its name are recorded.
Overview
CADD: Combined Annotation-Dependent Depletion: a genome-wide variant deleteriousness score that integrates more than 60 genomic features in a machine learning model trained to separate simulated de novo variants from variants fixed in human populations since the human-chimpanzee split. It scores single nucleotide variants and short insertions and deletions anywhere in the reference assembly, not only missense variants.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
1 evaluation · 1 result. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: CADD (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | 41.4% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 814/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ63) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI63 (row 'CADD', column 'rank_score') |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Use this configuration
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
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
0 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|
No evidence rows match these filters. Choose another scope or clear the search.
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record 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
Technical metadata and extraction receipts
Stable ID: vep-lit-20261014-config-livesey2025-cadd-unversioned
- areas
- dna-genomes; proteins-complexes
- contexts
- research; clinical_research
- method types
- supervised_machine_learning
- reported name
- CADD
- foundation model eligible
- false
- configuration type
- paper_evaluation
- source locator
- Supplementary Material 2, Table S8 column A ('CADD')
- missing metadata
- training overlap: reason: unreported; note: Not classed in Table S2; version: reason: unreported; note: Table S8 prints 'CADD' and Table S2 has no row for it; Table S2 lists CADD 1.6 (dbNSFP) and CADD 1.7 (download) separately and Table S8 also prints CADD_1.7
- 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
- CADD as scored in the Livesey and Marsh 2025 VEP benchmark.