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ESM1b minimum-LLR stop-gain score (Brandes et al. 2023)

ESM-1b stop-gain score: the lowest missense log-likelihood ratio among all possible missense variants in the protein region lost after the new stop codon.

3 evaluations · 3 results

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3 evaluations · 3 results. Different protocols are not a single leaderboard.

Protocol: ClinVar stop-gain pathogenicity by NMD status, ROC-AUC (Brandes et al. 2023 Fig. 6d, Supplementary Table 2)

Sorted by AUROC (ROC-AUC, pathogenic versus benign ClinVar all stop-gains; zero-shot) (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 (ROC-AUC, pathogenic versus benign ClinVar all stop-gains; zero-shot)	AUROC (ROC-AUC, pathogenic versus benign ClinVar stop-gains expected to undergo NMD (50 bp rule); zero-shot)	AUROC (ROC-AUC, pathogenic versus benign ClinVar stop-gains not expected to undergo NMD (50 bp rule); zero-shot)
ESM1b minimum-LLR stop-gain score (Brandes et al. 2023)Evaluation	ClinVar stop-gain variants, pathogenic vs benign (Brandes et al. 2023)	0.683	Not reported	Not reported
ESM1b minimum-LLR stop-gain score (Brandes et al. 2023)Evaluation	ClinVar stop-gains expected to undergo NMD (Brandes et al. 2023)	Not reported	0.566	Not reported
ESM1b minimum-LLR stop-gain score (Brandes et al. 2023)Evaluation	ClinVar stop-gains not expected to undergo NMD (Brandes et al. 2023)	Not reported	Not reported	0.734

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESM1b minimum-LLR stop-gain score (Brandes et al. 2023)	Protocol: ClinVar stop-gain pathogenicity by NMD status, ROC-AUC (Brandes et al. 2023 Fig. 6d, Supplementary Table 2) Dataset: ClinVar stop-gain variants, pathogenic vs benign (Brandes et al. 2023)	0.683 AUROC (ROC-AUC, pathogenic versus benign ClinVar all stop-gains; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b-minLLR on all stop-gains (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-stop-gains Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_stop_gains' cell D2, row 'ESM1b-minLLR', column 'AUC_ALL'
Configuration: ESM1b minimum-LLR stop-gain score (Brandes et al. 2023)	Protocol: ClinVar stop-gain pathogenicity by NMD status, ROC-AUC (Brandes et al. 2023 Fig. 6d, Supplementary Table 2) Dataset subset: ClinVar stop-gains expected to undergo NMD (Brandes et al. 2023)	0.566 AUROC (ROC-AUC, pathogenic versus benign ClinVar stop-gains expected to undergo NMD (50 bp rule); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b-minLLR on stop-gains expected to undergo NMD (50 bp rule) (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-stop-gains Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_stop_gains' cell C2, row 'ESM1b-minLLR', column 'AUC_NMD'
Configuration: ESM1b minimum-LLR stop-gain score (Brandes et al. 2023)	Protocol: ClinVar stop-gain pathogenicity by NMD status, ROC-AUC (Brandes et al. 2023 Fig. 6d, Supplementary Table 2) Dataset subset: ClinVar stop-gains not expected to undergo NMD (Brandes et al. 2023)	0.734 AUROC (ROC-AUC, pathogenic versus benign ClinVar stop-gains not expected to undergo NMD (50 bp rule); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b-minLLR on stop-gains not expected to undergo NMD (50 bp rule) (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-stop-gains Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_stop_gains' cell B2, row 'ESM1b-minLLR', column 'AUC_no_NMD'

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 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)

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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-esm1b-config-esm1b-minllr

areas: protein-function
contexts: clinical_research
method types: foundation_model
reported name: ESM1b-minLLR
version: esm1b_t33_650M_UR50S
parameters: esm1b_t33_650M_UR50S missense LLRs over the whole protein (sliding windows above 1,022 amino acids); minimum over the lost region
foundation model eligible: true
source locator: Methods 'Generalized effect scores for indels and stop-gain variants' paragraph 4; Supplementary Table 2 sheet 'Table_of_results_stop_gains' row 'ESM1b-minLLR'

Related records

configuration of: ESM-1b
system: ESM1b-minLLR on all stop-gains (Brandes et al. 2023)
system: ESM1b-minLLR on stop-gains expected to undergo NMD (50 bp rule) (Brandes et al. 2023)
system: ESM1b-minLLR on stop-gains not expected to undergo NMD (50 bp rule) (Brandes et al. 2023)

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