Dataset

ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)

1,791 pathogenic and 1,679 benign in-frame insertions, deletions and deletion-insertions with at least one ClinVar gold star, mapped to RefSeq protein sequences.

Evaluation results

7 evaluations · 7 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
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: 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'
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'

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

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Missing or unresolved evidence

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Verified: Not verified

Evidence incomplete

Investigate discrepancies

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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

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Missing or unresolved evidence

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File checksums match the recorded files: not yet verified
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Score meaning and direction are confirmed: 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

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Dataset and evaluation context

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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.

14 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
Denominator 3470 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 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend 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 3470 Context-only references	Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Original source ↗ Supplementary Methods 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend 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 ClinVar in-frame indels with at least one gold star; 17 with mismatching RefSeq sequences and 24 duplicates or with non-standard amino acids removed 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 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend 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 ClinVar in-frame indels with at least one gold star; 17 with mismatching RefSeq sequences and 24 duplicates or with non-standard amino acids removed Context-only references	Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Original source ↗ Supplementary Methods 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend 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 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend 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 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend 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 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend Context-only references	Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Original source ↗ Supplementary Methods 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend 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; no training on labels 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 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend 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; no training on labels Context-only references	Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Original source ↗ Supplementary Methods 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend 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
Version ClinVar variant_summary.txt.gz downloaded 2023-01-24 (GRCh38) 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 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend 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.version` Source artifact SHA-256: `919ca366369efbe7e0880565192de127375edddedb1aa43ad023dec612bb4a04` Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-pmc10484790.xml.gz Inspected artifact
Version ClinVar variant_summary.txt.gz downloaded 2023-01-24 (GRCh38) Context-only references	Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Original source ↗ Supplementary Methods 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend 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.version` 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-clinvar-inframe-indels

areas: dna-genomes; protein-function
contexts: clinical_research
version: ClinVar variant_summary.txt.gz downloaded 2023-01-24 (GRCh38)
split: Whole labelled set; no training on labels
population: ClinVar in-frame indels with at least one gold star; 17 with mismatching RefSeq sequences and 24 duplicates or with non-standard amino acids removed
denominator: 3470
source locator: Supplementary Methods 'Indels and stop gain ClinVar benchmarks' paragraph 1; Fig. 6a,b legend

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