Dataset subset

HGMD/gnomAD missense variants scored by both ESM1b and VARITY_ER (Brandes et al. 2023)

The 87,359 variants of the HGMD/gnomAD missense benchmark that have both an ESM1b and a VARITY_ER score.

Evaluation results

2 evaluations · 4 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, ESM1b head to head with one other method on the variants both score (Brandes et al. 2023 Fig. 2g,h, Supplementary Table 2) Dataset subset: HGMD/gnomAD missense variants scored by both ESM1b and VARITY_ER (Brandes et al. 2023)	0.906 AUPRC (balanced PRC-AUC over the variants both methods score: 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, head to head against VARITY_ER (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-head-to-head 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 H45, row 'VARITY_ER', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: HGMD/gnomAD missense pathogenicity, ESM1b head to head with one other method on the variants both score (Brandes et al. 2023 Fig. 2g,h, Supplementary Table 2) Dataset subset: HGMD/gnomAD missense variants scored by both ESM1b and VARITY_ER (Brandes et al. 2023)	0.894 AUROC (global ROC-AUC over the variants both methods score; 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, head to head against VARITY_ER (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-head-to-head 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 F45, row 'VARITY_ER', column 'head2head_ESM1b_auc_AUROC'
Configuration: VARITY_ER (Brandes et al. 2023 head-to-head comparison)	Protocol: HGMD/gnomAD missense pathogenicity, ESM1b head to head with one other method on the variants both score (Brandes et al. 2023 Fig. 2g,h, Supplementary Table 2) Dataset subset: HGMD/gnomAD missense variants scored by both ESM1b and VARITY_ER (Brandes et al. 2023)	0.932 AUPRC (balanced PRC-AUC over the variants both methods score: 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 VARITY_ER on HGMD/gnomAD missense, head to head against ESM1b (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-head-to-head 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 G45, row 'VARITY_ER', column 'head2head_VEP_auc_Balanced_AUPRC'
Configuration: VARITY_ER (Brandes et al. 2023 head-to-head comparison)	Protocol: HGMD/gnomAD missense pathogenicity, ESM1b head to head with one other method on the variants both score (Brandes et al. 2023 Fig. 2g,h, Supplementary Table 2) Dataset subset: HGMD/gnomAD missense variants scored by both ESM1b and VARITY_ER (Brandes et al. 2023)	0.929 AUROC (global ROC-AUC over the variants both methods score; 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 VARITY_ER on HGMD/gnomAD missense, head to head against ESM1b (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-head-to-head 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 E45, row 'VARITY_ER', column 'head2head_VEP_auc_AUROC'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Readiness checks, gaps and artifacts

Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

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Verified: Not verified

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Subset and evaluation context

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Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

8 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Scored count 87359 Context-only references	Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Original source ↗ Supplementary Table 2 sheet 'Table_of_results_HGMD' cell I45, row 'VARITY_ER', column 'head2head_n_variants' 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.scored_count` Source artifact SHA-256: `093c32e4156a801c0dd809a437c87818a4f1d04df92e037cf40222471a3e72e2` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz Inspected artifact
Source dataset label HGMD/gnomAD Context-only references	Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Original source ↗ Supplementary Table 2 sheet 'Table_of_results_HGMD' cell I45, row 'VARITY_ER', column 'head2head_n_variants' 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_dataset_label` Source artifact SHA-256: `093c32e4156a801c0dd809a437c87818a4f1d04df92e037cf40222471a3e72e2` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz Inspected artifact
Source location Supplementary Table 2 sheet 'Table_of_results_HGMD' cell I45, row 'VARITY_ER', column 'head2head_n_variants' Context-only references	Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Original source ↗ Supplementary Table 2 sheet 'Table_of_results_HGMD' cell I45, row 'VARITY_ER', column 'head2head_n_variants' 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: `093c32e4156a801c0dd809a437c87818a4f1d04df92e037cf40222471a3e72e2` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz Inspected artifact
Split Whole labelled set restricted to variants scored by both methods Context-only references	Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Original source ↗ Supplementary Table 2 sheet 'Table_of_results_HGMD' cell I45, row 'VARITY_ER', column 'head2head_n_variants' 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: `093c32e4156a801c0dd809a437c87818a4f1d04df92e037cf40222471a3e72e2` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz Inspected artifact
Subset scope Variants with both ESM1b and VARITY_ER scores Context-only references	Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Original source ↗ Supplementary Table 2 sheet 'Table_of_results_HGMD' cell I45, row 'VARITY_ER', column 'head2head_n_variants' 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.subset_scope` Source artifact SHA-256: `093c32e4156a801c0dd809a437c87818a4f1d04df92e037cf40222471a3e72e2` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz Inspected artifact
Description The 87,359 variants of the HGMD/gnomAD missense benchmark that have both an ESM1b and a VARITY_ER score. Context-only references	Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Original source ↗ Supplementary Table 2 sheet 'Table_of_results_HGMD' cell I45, row 'VARITY_ER', column 'head2head_n_variants' 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: `description` Source artifact SHA-256: `093c32e4156a801c0dd809a437c87818a4f1d04df92e037cf40222471a3e72e2` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz Inspected artifact
Relationship: used in gfm-guides-20261014-esm1b-protocol-hgmd-head-to-head Context-only references	Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Original source ↗ Supplementary Table 2 sheet 'Table_of_results_HGMD' cell I45, row 'VARITY_ER', column 'head2head_n_variants' 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: `links:used_in:gfm-guides-20261014-esm1b-protocol-hgmd-head-to-head` Source artifact SHA-256: `093c32e4156a801c0dd809a437c87818a4f1d04df92e037cf40222471a3e72e2` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz Inspected artifact
Name HGMD/gnomAD missense variants scored by both ESM1b and VARITY_ER (Brandes et al. 2023) Context-only references	Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Original source ↗ Supplementary Table 2 sheet 'Table_of_results_HGMD' cell I45, row 'VARITY_ER', column 'head2head_n_variants' 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: `name` Source artifact SHA-256: `093c32e4156a801c0dd809a437c87818a4f1d04df92e037cf40222471a3e72e2` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz Inspected artifact

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Sources and history

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

1 source record and release history

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-data-hgmd-h2h-varity-er

areas: dna-genomes; protein-function
contexts: clinical_research
split: Whole labelled set restricted to variants scored by both methods
scored count: 87359
source dataset label: HGMD/gnomAD
subset scope: Variants with both ESM1b and VARITY_ER scores
source locator: Supplementary Table 2 sheet 'Table_of_results_HGMD' cell I45, row 'VARITY_ER', column 'head2head_n_variants'
missing metadata: version: reason: unreported; note: Download dates of the EVE-portal ClinVar file and HGMD release not printed

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