Brandes et al. 2023 ClinVar in-frame indel and stop-gain pathogenicity benchmarks
ROC-AUC of ESM1b-based scores, CADD and simple baselines for pathogenic versus benign ClinVar in-frame indels and stop-gain variants.
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Overview
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Results on linked records
This benchmark has no results of its own in this release. 2 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.
- ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Protocol · part of this benchmark · 16 evaluations · 16 results
- ClinVar stop-gain pathogenicity by NMD status, ROC-AUC (Brandes et al. 2023 Fig. 6d, Supplementary Table 2) Protocol · part of this benchmark · 10 evaluations · 10 results
Methods and evaluation design
Procedure, tasks and evaluated configurations
Baseline coverage
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Baseline status by linked protocol
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
3 source records and release history
- Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) · Original source · Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10)
- Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Original source · Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10)
- Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) · Original source · Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10)
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-esm1b-benchmark-brandes2023-clinvar-multiresidue
- areas
- dna-genomes; protein-function
- contexts
- clinical_research
- entity level
- suite
- version
- Nature Genetics 2023 version of record
- task
- Pathogenicity classification of in-frame indels and stop-gain variants
- scope note
- Two ClinVar-derived labelled sets built by the authors. Only CADD among published predictors is compared on indels, because most indel predictors are trained on ClinVar; no published predictor is compared on stop-gains.
- source locator
- Results 'ESM1b can predict the effects of multiresidue variants' and Fig. 6 legend; Methods 'Generalized effect scores for indels and stop-gain variants', 'Baseline scores of indel and stop-gain variant effects'; Supplementary Methods 'Indels and stop gain ClinVar benchmarks'