Dataset subset

ClinVar missense variants scored by both ESM1b and FATHMM (Brandes et al. 2023)

The 38,150 variants of the ClinVar missense benchmark that have both an ESM1b and a FATHMM score.

Evaluation results

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

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

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: ClinVar 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: ClinVar missense variants scored by both ESM1b and FATHMM (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 ClinVar missense, head to head against FATHMM (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-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_ClinVar' cell H29, row 'FATHMM', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and FATHMM (Brandes et al. 2023)	0.906 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 ClinVar missense, head to head against FATHMM (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-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_ClinVar' cell F29, row 'FATHMM', column 'head2head_ESM1b_auc_AUROC'
Configuration: FATHMM (Brandes et al. 2023 head-to-head comparison)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and FATHMM (Brandes et al. 2023)	0.801 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 FATHMM on ClinVar missense, head to head against ESM1b (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-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_ClinVar' cell G29, row 'FATHMM', column 'head2head_VEP_auc_Balanced_AUPRC'
Configuration: FATHMM (Brandes et al. 2023 head-to-head comparison)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and FATHMM (Brandes et al. 2023)	0.788 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 FATHMM on ClinVar missense, head to head against ESM1b (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-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_ClinVar' cell E29, row 'FATHMM', column 'head2head_VEP_auc_AUROC'

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

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

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

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

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File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified
Sample annotations are recorded: not yet verified
Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
A pinned run recipe exists: not yet verified
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Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Independent validation data exist: not yet verified
Overlap with training data is checked: not yet verified

Verified: Not verified

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Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Subset and evaluation context

This record describes a particular subset or cohort used in an evaluation. Its results do not describe the full dataset.

Evidence

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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.

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 38150 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_ClinVar' cell I29, row 'FATHMM', 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 ClinVar 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_ClinVar' cell I29, row 'FATHMM', 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_ClinVar' cell I29, row 'FATHMM', 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_ClinVar' cell I29, row 'FATHMM', 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_ClinVar' cell I29, row 'FATHMM', 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 FATHMM 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_ClinVar' cell I29, row 'FATHMM', 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 38,150 variants of the ClinVar missense benchmark that have both an ESM1b and a FATHMM 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_ClinVar' cell I29, row 'FATHMM', 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-clinvar-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_ClinVar' cell I29, row 'FATHMM', 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-clinvar-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 ClinVar missense variants scored by both ESM1b and FATHMM (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_ClinVar' cell I29, row 'FATHMM', 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

How to read the evidence

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-clinvar-h2h-fathmm

areas: dna-genomes; protein-function
contexts: clinical_research
split: Whole labelled set restricted to variants scored by both methods
scored count: 38150
source dataset label: ClinVar
subset scope: Variants with both ESM1b and FATHMM scores
source locator: Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell I29, row 'FATHMM', 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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