Configuration

Polyphen2 (HVAR) (Brandes et al. 2023 head-to-head comparison)

PolyPhen-2 HumVar-trained model: precomputed scores from dbNSFP 4.3a.

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

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

Sorted by 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) (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	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)	AUROC (global ROC-AUC over the variants both methods score; zero-shot)
Polyphen2 (HVAR) (Brandes et al. 2023 head-to-head comparison)Evaluation	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), HGMD/gnomAD missense variants scored by both ESM1b and Polyphen2 (HVAR) (Brandes et al. 2023)	0.874 (best in column)	0.883 (best in column)
Polyphen2 (HVAR) (Brandes et al. 2023 head-to-head comparison)Evaluation	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), ClinVar missense variants scored by both ESM1b and Polyphen2 (HVAR) (Brandes et al. 2023)	0.874	0.882

All 4 result rows with coverage, uncertainty and sources

Filter evaluations

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: Polyphen2 (HVAR) (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 Polyphen2 (HVAR) (Brandes et al. 2023)	0.874 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 Polyphen2 (HVAR) 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 G42, row 'Polyphen2 (HVAR)', column 'head2head_VEP_auc_Balanced_AUPRC'
Configuration: Polyphen2 (HVAR) (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 Polyphen2 (HVAR) (Brandes et al. 2023)	0.882 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 Polyphen2 (HVAR) 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 E42, row 'Polyphen2 (HVAR)', column 'head2head_VEP_auc_AUROC'
Configuration: Polyphen2 (HVAR) (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 Polyphen2 (HVAR) (Brandes et al. 2023)	0.874 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 Polyphen2 (HVAR) 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 G42, row 'Polyphen2 (HVAR)', column 'head2head_VEP_auc_Balanced_AUPRC'
Configuration: Polyphen2 (HVAR) (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 Polyphen2 (HVAR) (Brandes et al. 2023)	0.883 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 Polyphen2 (HVAR) 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 E42, row 'Polyphen2 (HVAR)', column 'head2head_VEP_auc_AUROC'

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

Use this configuration

How it works, versions and access

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

0 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

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

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)

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-esm1b-config-polyphen2-hvar

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: Polyphen2 (HVAR)
version: dbNSFP 4.3a
parameters: dbNSFP 4.3a score
foundation model eligible: false
training overlap: Excluded from the paper's main clinical comparison; Supplementary Table 2 note: 'Trained on HumVar'
source locator: Supplementary Table 2 column vep_name 'Polyphen2 (HVAR)' and column 'note'; Methods 'Other VEP methods'
provenance note: Scored head to head against ESM1b in Brandes et al. 2023 Supplementary Table 2 only; not part of the 19-method comparison in Fig. 2e,f.

Related records

configuration of: PolyPhen-2
system: Polyphen2 (HVAR) on ClinVar missense, head to head against ESM1b (Brandes et al. 2023)
system: Polyphen2 (HVAR) on HGMD/gnomAD missense, head to head against ESM1b (Brandes et al. 2023)

Suggest a correction