Dataset

HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)

HGMD high-confidence disease-causing (DM) missense variants versus gnomAD v2.1.1 exome missense variants with MAF > 0.01; 92,942 variants (70,714 pathogenic, 22,228 benign) on primary UniProt isoforms.

Evaluation results

19 evaluations · 38 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: bStatistic (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.534 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source bStatistic on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C19, row 'bStatistic', column 'AUC_Balanced_AUPRC'
Configuration: bStatistic (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.536 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source bStatistic on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B19, row 'bStatistic', column 'AUC_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.881 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); 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 on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C2, row 'ESM1b', column 'AUC_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.887 AUROC (global ROC-AUC over all variants; 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 on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B2, row 'ESM1b', column 'AUC_AUROC'
Configuration: EVE (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.881 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source EVE on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C3, row 'EVE', column 'AUC_Balanced_AUPRC'
Configuration: EVE (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.885 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source EVE on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B3, row 'EVE', column 'AUC_AUROC'
Configuration: fitCons (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.477 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source fitCons on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C20, row 'fitCons', column 'AUC_Balanced_AUPRC'
Configuration: fitCons (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.468 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source fitCons on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B20, row 'fitCons', column 'AUC_AUROC'
Configuration: GenoCanyon (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.734 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GenoCanyon on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C12, row 'GenoCanyon', column 'AUC_Balanced_AUPRC'
Configuration: GenoCanyon (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.725 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GenoCanyon on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B12, row 'GenoCanyon', column 'AUC_AUROC'
Configuration: GERP++ (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.645 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GERP++ on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C15, row 'GERP++', column 'AUC_Balanced_AUPRC'
Configuration: GERP++ (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.7 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GERP++ on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B15, row 'GERP++', column 'AUC_AUROC'
Configuration: LRT (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.787 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LRT on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C10, row 'LRT', column 'AUC_Balanced_AUPRC'
Configuration: LRT (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.76 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LRT on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B10, row 'LRT', column 'AUC_AUROC'
Configuration: MTBAN (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.856 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MTBAN on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C8, row 'MTBAN', column 'AUC_Balanced_AUPRC'
Configuration: MTBAN (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.843 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MTBAN on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B8, row 'MTBAN', column 'AUC_AUROC'
Configuration: MutationAssessor (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.876 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MutationAssessor on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C5, row 'MutationAssessor', column 'AUC_Balanced_AUPRC'
Configuration: MutationAssessor (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.879 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MutationAssessor on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B5, row 'MutationAssessor', column 'AUC_AUROC'
Configuration: phastCons (mammalian) (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.675 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phastCons (mammalian) on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C17, row 'phastCons (mammalian)', column 'AUC_Balanced_AUPRC'
Configuration: phastCons (mammalian) (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.666 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phastCons (mammalian) on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B17, row 'phastCons (mammalian)', column 'AUC_AUROC'
Configuration: phastCons (primate) (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.624 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phastCons (primate) on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C18, row 'phastCons (primate)', column 'AUC_Balanced_AUPRC'
Configuration: phastCons (primate) (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.645 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phastCons (primate) on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B18, row 'phastCons (primate)', column 'AUC_AUROC'
Configuration: phastCons (vertebrate) (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.791 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phastCons (vertebrate) on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C14, row 'phastCons (vertebrate)', column 'AUC_Balanced_AUPRC'
Configuration: phastCons (vertebrate) (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.712 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phastCons (vertebrate) on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell B14, row 'phastCons (vertebrate)', column 'AUC_AUROC'
Configuration: phyloP (mammalian) (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023)	0.68 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phyloP (mammalian) on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-all-19-methods 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_HGMD' cell C13, row 'phyloP (mammalian)', column 'AUC_Balanced_AUPRC'

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Access HGMD requires an access request; not public Context-only references	Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Original source ↗ Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) Retrieved: 2026-10-14T12:03:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.access` Source artifact SHA-256: `919ca366369efbe7e0880565192de127375edddedb1aa43ad023dec612bb4a04` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-pmc10484790.xml.gz Inspected artifact
Access HGMD requires an access request; not public Context-only references	Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Original source ↗ Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) Retrieved: 2026-10-14T12:03:21Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.access` Source artifact SHA-256: `30f1c2713875c7cec40f0beee19864840bc55326ddf68918841f93f8bb897c2a` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-information.pdf.gz Inspected artifact
Denominator 92942 Context-only references	Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Original source ↗ Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) Retrieved: 2026-10-14T12:03:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.denominator` Source artifact SHA-256: `919ca366369efbe7e0880565192de127375edddedb1aa43ad023dec612bb4a04` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-pmc10484790.xml.gz Inspected artifact
Denominator 92942 Context-only references	Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Original source ↗ Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) Retrieved: 2026-10-14T12:03:21Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.denominator` Source artifact SHA-256: `30f1c2713875c7cec40f0beee19864840bc55326ddf68918841f93f8bb897c2a` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-information.pdf.gz Inspected artifact
Population HGMD DM missense variants versus gnomAD missense variants with MAF > 0.01, primary UniProt isoforms Context-only references	Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Original source ↗ Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) Retrieved: 2026-10-14T12:03:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `919ca366369efbe7e0880565192de127375edddedb1aa43ad023dec612bb4a04` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-pmc10484790.xml.gz Inspected artifact
Population HGMD DM missense variants versus gnomAD missense variants with MAF > 0.01, primary UniProt isoforms Context-only references	Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Original source ↗ Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) Retrieved: 2026-10-14T12:03:21Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `30f1c2713875c7cec40f0beee19864840bc55326ddf68918841f93f8bb897c2a` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-information.pdf.gz Inspected artifact
Source location Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Context-only references	Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Original source ↗ Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) Retrieved: 2026-10-14T12:03:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `919ca366369efbe7e0880565192de127375edddedb1aa43ad023dec612bb4a04` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-pmc10484790.xml.gz Inspected artifact
Source location Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Context-only references	Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Original source ↗ Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) Retrieved: 2026-10-14T12:03:21Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `30f1c2713875c7cec40f0beee19864840bc55326ddf68918841f93f8bb897c2a` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-information.pdf.gz Inspected artifact
Split Whole labelled set Context-only references	Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Original source ↗ Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) Retrieved: 2026-10-14T12:03:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `919ca366369efbe7e0880565192de127375edddedb1aa43ad023dec612bb4a04` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-pmc10484790.xml.gz Inspected artifact
Split Whole labelled set Context-only references	Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Original source ↗ Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) Retrieved: 2026-10-14T12:03:21Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `30f1c2713875c7cec40f0beee19864840bc55326ddf68918841f93f8bb897c2a` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-information.pdf.gz Inspected artifact

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Sources and history

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

2 source records and release history

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)
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)

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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-esm1b-data-hgmd-dm-vs-gnomad-common-missense

areas: dna-genomes; protein-function
contexts: clinical_research
version: HGMD full dataset (access on request; release not printed); gnomAD v2.1.1 exomes (PASS, AN > 200,000)
split: Whole labelled set
population: HGMD DM missense variants versus gnomAD missense variants with MAF > 0.01, primary UniProt isoforms
denominator: 92942
access: HGMD requires an access request; not public
source locator: Supplementary Methods 'Clinical benchmarks of missense variants (ClinVar and HGMD/gnomAD)' paragraphs 2-4

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