Protocol

ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2)

Global ROC-AUC of each indel score for pathogenic versus benign ClinVar in-frame indels, over all indels and by indel type.

16 evaluations · 16 results

Overview

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

16 recorded evaluations, 16 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

16 evaluations · 16 results. Different protocols are not a single leaderboard.

Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2)

Sorted by AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; 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 in-frame indels; zero-shot)	AUROC (ROC-AUC, pathogenic versus benign ClinVar deletion-insertions; zero-shot)	AUROC (ROC-AUC, pathogenic versus benign ClinVar deletions; zero-shot)	AUROC (ROC-AUC, pathogenic versus benign ClinVar insertions; zero-shot)
ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.874 (best in column)	Not reported	Not reported	Not reported
ESM1b PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.869	Not reported	Not reported	Not reported
ESM1b weighted PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.861	Not reported	Not reported	Not reported
CADD in-frame indel scores (Brandes et al. 2023)Evaluation	ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.836	Not reported	Not reported	Not reported
Pairwise alignment score (indel baseline)Evaluation	ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.586	Not reported	Not reported	Not reported
BlastP score (indel baseline)Evaluation	ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.582	Not reported	Not reported	Not reported
LevenshteinEvaluation	ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.502	Not reported	Not reported	Not reported
CADD in-frame indel scores (Brandes et al. 2023)Evaluation	ClinVar in-frame deletions (Brandes et al. 2023)	Not reported	Not reported	0.848	Not reported
ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame deletions (Brandes et al. 2023)	Not reported	Not reported	0.875 (best in column)	Not reported
ESM1b PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame deletions (Brandes et al. 2023)	Not reported	Not reported	0.869	Not reported
CADD in-frame indel scores (Brandes et al. 2023)Evaluation	ClinVar in-frame deletion-insertions (Brandes et al. 2023)	Not reported	0.671	Not reported	Not reported
ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame deletion-insertions (Brandes et al. 2023)	Not reported	0.887 (best in column)	Not reported	Not reported
ESM1b PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame deletion-insertions (Brandes et al. 2023)	Not reported	0.857	Not reported	Not reported
CADD in-frame indel scores (Brandes et al. 2023)Evaluation	ClinVar in-frame insertions (Brandes et al. 2023)	Not reported	Not reported	Not reported	0.757
ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame insertions (Brandes et al. 2023)	Not reported	Not reported	Not reported	0.831
ESM1b PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame insertions (Brandes et al. 2023)	Not reported	Not reported	Not reported	0.859 (best in column)

All 16 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
Method: BlastP score (indel baseline)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset: ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.582 AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; 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 BlastP on all in-frame indels (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell B7, row 'BlastP', column 'AUC_indels'
Configuration: CADD in-frame indel scores (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset: ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.836 AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; 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 CADD on all in-frame indels (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell B5, row 'CADD', column 'AUC_indels'
Configuration: CADD in-frame indel scores (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame deletions (Brandes et al. 2023)	0.848 AUROC (ROC-AUC, pathogenic versus benign ClinVar deletions; 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 CADD on deletions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell D5, row 'CADD', column 'AUC_del'
Configuration: ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame deletions (Brandes et al. 2023)	0.875 AUROC (ROC-AUC, pathogenic versus benign ClinVar deletions; 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-aPLLR on deletions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell D2, row 'ESM1b-aPLLR', column 'AUC_del'
Configuration: ESM1b PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame deletions (Brandes et al. 2023)	0.869 AUROC (ROC-AUC, pathogenic versus benign ClinVar deletions; 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-PLLR on deletions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell D3, row 'ESM1b-PLLR', column 'AUC_del'
Configuration: CADD in-frame indel scores (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame deletion-insertions (Brandes et al. 2023)	0.671 AUROC (ROC-AUC, pathogenic versus benign ClinVar deletion-insertions; 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 CADD on deletion-insertions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell E5, row 'CADD', column 'AUC_delins'
Configuration: ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame deletion-insertions (Brandes et al. 2023)	0.887 AUROC (ROC-AUC, pathogenic versus benign ClinVar deletion-insertions; 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-aPLLR on deletion-insertions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell E2, row 'ESM1b-aPLLR', column 'AUC_delins'
Configuration: ESM1b PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame deletion-insertions (Brandes et al. 2023)	0.857 AUROC (ROC-AUC, pathogenic versus benign ClinVar deletion-insertions; 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-PLLR on deletion-insertions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell E3, row 'ESM1b-PLLR', column 'AUC_delins'
Configuration: ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset: ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.874 AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; 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-aPLLR on all in-frame indels (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell B2, row 'ESM1b-aPLLR', column 'AUC_indels'
Configuration: ESM1b PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset: ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.869 AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; 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-PLLR on all in-frame indels (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell B3, row 'ESM1b-PLLR', column 'AUC_indels'
Configuration: ESM1b weighted PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset: ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.861 AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; 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-wPLLR on all in-frame indels (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell B4, row 'ESM1b-wPLLR', column 'AUC_indels'
Configuration: CADD in-frame indel scores (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame insertions (Brandes et al. 2023)	0.757 AUROC (ROC-AUC, pathogenic versus benign ClinVar insertions; 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 CADD on insertions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell C5, row 'CADD', column 'AUC_ins'
Configuration: ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame insertions (Brandes et al. 2023)	0.831 AUROC (ROC-AUC, pathogenic versus benign ClinVar insertions; 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-aPLLR on insertions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell C2, row 'ESM1b-aPLLR', column 'AUC_ins'
Configuration: ESM1b PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame insertions (Brandes et al. 2023)	0.859 AUROC (ROC-AUC, pathogenic versus benign ClinVar insertions; 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-PLLR on insertions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell C3, row 'ESM1b-PLLR', column 'AUC_ins'
Method: Levenshtein	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset: ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.502 AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; 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 Edit distance on all in-frame indels (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell B8, row 'Edit distance', column 'AUC_indels'
Method: Pairwise alignment score (indel baseline)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset: ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.586 AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; 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 Alignment on all in-frame indels (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell B6, row 'Alignment', column 'AUC_indels'

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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-protocol-clinvar-inframe-indels

areas: dna-genomes; protein-function
contexts: clinical_research
protocol: Scores used directly (no training on these labels); every method scored on the same 3,470 indels. ESM1b scores are pseudo-log-likelihood ratios between mutated and wild-type sequences; baselines score sequence dissimilarity.
version: Supplementary Table 2 sheet 'Table_of_results_indels'
metric: auroc
metric direction: higher
unit: unitless
denominator: 3470
limitations: Benchmark built by the ESM1b workflow's authors (author-reported for ESM1b and the baselines).; CADD is the only published predictor compared; the others that score indels are trained on ClinVar.; Per-type ROC-AUCs are printed only for the three ESM1b PLLR scores where available and CADD; the workbook leaves the other cells 'NaN'.
source locator: Results 'ESM1b can predict the effects of multiresidue variants', paragraph beginning 'We compared ESM1b to other models'; Methods 'Generalized effect scores for indels and stop-gain variants' and 'Baseline scores of indel and stop-gain variant effects'; Supplementary Table 2 'Contents'

Related records

part of: Brandes et al. 2023 ClinVar in-frame indel and stop-gain pathogenicity benchmarks
uses data: ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)
assessment: BlastP on all in-frame indels (Brandes et al. 2023)
assessment: CADD on all in-frame indels (Brandes et al. 2023)
assessment: CADD on deletions (Brandes et al. 2023)
assessment: ESM1b-aPLLR on deletions (Brandes et al. 2023)
assessment: ESM1b-PLLR on deletions (Brandes et al. 2023)
assessment: CADD on deletion-insertions (Brandes et al. 2023)
assessment: ESM1b-aPLLR on deletion-insertions (Brandes et al. 2023)
assessment: ESM1b-PLLR on deletion-insertions (Brandes et al. 2023)
assessment: ESM1b-aPLLR on all in-frame indels (Brandes et al. 2023)
assessment: ESM1b-PLLR on all in-frame indels (Brandes et al. 2023)
assessment: ESM1b-wPLLR on all in-frame indels (Brandes et al. 2023)
assessment: CADD on insertions (Brandes et al. 2023)
assessment: ESM1b-aPLLR on insertions (Brandes et al. 2023)
assessment: ESM1b-PLLR on insertions (Brandes et al. 2023)
assessment: Edit distance on all in-frame indels (Brandes et al. 2023)
assessment: Alignment on all in-frame indels (Brandes et al. 2023)

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