Evaluation

GERP++_RS_b on the BRCA2 functional truth set (Cubuk et al. 2021)

Published in silico evidence comparison for BRCA1/BRCA2 missense variants; transcribed, not reproduced.

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Release 2026-10-10-84341e0b121f · Evidence verified: Not verified

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Evaluation results

1 evaluation · 3 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: GERP++_RS_b (Cubuk et al. 2021)	Protocol: BRCA2 functional truth set, binary in silico calls (Cubuk et al. 2021) Dataset: BRCA2 functional truth set: 188 missense variants classed deleterious or tolerated by Homology-directed repair	5.98 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (5.43-6.58) has the same log-scale width as this row's positive likelihood ratio interval and is not consistent with the Supplementary Table 6 counts; kept in printed_source_cell only. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GERP++_RS_b on the BRCA2 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca2 Aggregation: Not reported Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes; Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) · Supplementary Table 9 (sheet 'SupTable9_Likelihood_Ratios'), I53; tool 'GERP++_RS_b'; column 'BRCA2_negative_LR'
Configuration: GERP++_RS_b (Cubuk et al. 2021)	Protocol: BRCA2 functional truth set, binary in silico calls (Cubuk et al. 2021) Dataset: BRCA2 functional truth set: 188 missense variants classed deleterious or tolerated by Homology-directed repair	2 false-negative-count count · lower Uncertainty: Not applicable: Count Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GERP++_RS_b on the BRCA2 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca2 Aggregation: Not reported Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes; Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) · Supplementary Table 6 (sheet 'SupTable6_Tool_Counts'), U23; tool 'GERP++_RS_b'; column 'BRCA2_FN'
Configuration: GERP++_RS_b (Cubuk et al. 2021)	Protocol: BRCA2 functional truth set, binary in silico calls (Cubuk et al. 2021) Dataset: BRCA2 functional truth set: 188 missense variants classed deleterious or tolerated by Homology-directed repair	1.19 likelihood-ratio unitless · higher Uncertainty: CI 1.08 to 1.31. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GERP++_RS_b on the BRCA2 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca2 Aggregation: Not reported Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes; Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) · Supplementary Table 9 (sheet 'SupTable9_Likelihood_Ratios'), H53; tool 'GERP++_RS_b'; column 'BRCA2_positive_LR'

Source checking is not independent reproduction. Release 2026-10-10-84341e0b121f.

Evaluation procedure

brca-20261009-protocol-cubuk2021-brca2

Configuration: GERP++_RS_b (Cubuk et al. 2021)
Protocol: BRCA2 functional truth set, binary in silico calls (Cubuk et al. 2021)
Dataset: BRCA2 functional truth set: 188 missense variants classed deleterious or tolerated by Homology-directed repair

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-09
protocol id: brca-20261009-protocol-cubuk2021-brca2
dataset version: Not reported
split: Whole truth set
population: 187 of 188 BRCA2 truth-set variants with a deleterious or tolerated call
inputs: Missense variant
adaptation: Not reported
metric implementation: Binary call at the Supplementary Table 5 threshold; PLR = TPR/FPR and likelihood ratio for benignity = TNR/FNR (Supplementary Table 7)
aggregation: Pooled over variants
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Whole truth set
Adaptation: Not reported
Scoring implementation: Binary call at the Supplementary Table 5 threshold; PLR = TPR/FPR and likelihood ratio for benignity = TNR/FNR (Supplementary Table 7)

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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36 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-84341e0b121f
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation Not reported Context-only references	Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes Original source ↗ Supplementary Table 9 row 53 and Supplementary Table 6 row 23, tool 'GERP++_RS_b', BRCA2 columns Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genetics in Medicine 23(11):2096, published 2021-07-06; PMC8553612 full-text XML Retrieved: 2026-10-09T21:18:04Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `ea6391e04f5f01353bb611fd45437f21c531848cf3e93b288bdc52494efc90ae` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.adaptation Not reported Context-only references	Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) Original source ↗ Supplementary Table 9 row 53 and Supplementary Table 6 row 23, tool 'GERP++_RS_b', BRCA2 columns Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41436_2021_1265_MOESM3_ESM.xlsx Retrieved: 2026-10-09T21:18:15Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `02df1b0dbf916d598dd8278ba45091022bf78c5722ac13a07d5b1b70d64dc179` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation Pooled over variants Context-only references	Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes Original source ↗ Supplementary Table 9 row 53 and Supplementary Table 6 row 23, tool 'GERP++_RS_b', BRCA2 columns Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genetics in Medicine 23(11):2096, published 2021-07-06; PMC8553612 full-text XML Retrieved: 2026-10-09T21:18:04Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `ea6391e04f5f01353bb611fd45437f21c531848cf3e93b288bdc52494efc90ae` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation Pooled over variants Context-only references	Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) Original source ↗ Supplementary Table 9 row 53 and Supplementary Table 6 row 23, tool 'GERP++_RS_b', BRCA2 columns Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41436_2021_1265_MOESM3_ESM.xlsx Retrieved: 2026-10-09T21:18:15Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `02df1b0dbf916d598dd8278ba45091022bf78c5722ac13a07d5b1b70d64dc179` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes Original source ↗ Supplementary Table 9 row 53 and Supplementary Table 6 row 23, tool 'GERP++_RS_b', BRCA2 columns Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genetics in Medicine 23(11):2096, published 2021-07-06; PMC8553612 full-text XML Retrieved: 2026-10-09T21:18:04Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `ea6391e04f5f01353bb611fd45437f21c531848cf3e93b288bdc52494efc90ae` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) Original source ↗ Supplementary Table 9 row 53 and Supplementary Table 6 row 23, tool 'GERP++_RS_b', BRCA2 columns Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41436_2021_1265_MOESM3_ESM.xlsx Retrieved: 2026-10-09T21:18:15Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `02df1b0dbf916d598dd8278ba45091022bf78c5722ac13a07d5b1b70d64dc179` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version Not reported Context-only references	Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes Original source ↗ Supplementary Table 9 row 53 and Supplementary Table 6 row 23, tool 'GERP++_RS_b', BRCA2 columns Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genetics in Medicine 23(11):2096, published 2021-07-06; PMC8553612 full-text XML Retrieved: 2026-10-09T21:18:04Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `ea6391e04f5f01353bb611fd45437f21c531848cf3e93b288bdc52494efc90ae` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version Not reported Context-only references	Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) Original source ↗ Supplementary Table 9 row 53 and Supplementary Table 6 row 23, tool 'GERP++_RS_b', BRCA2 columns Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41436_2021_1265_MOESM3_ESM.xlsx Retrieved: 2026-10-09T21:18:15Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `02df1b0dbf916d598dd8278ba45091022bf78c5722ac13a07d5b1b70d64dc179` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs Missense variant Context-only references	Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes Original source ↗ Supplementary Table 9 row 53 and Supplementary Table 6 row 23, tool 'GERP++_RS_b', BRCA2 columns Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genetics in Medicine 23(11):2096, published 2021-07-06; PMC8553612 full-text XML Retrieved: 2026-10-09T21:18:04Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `ea6391e04f5f01353bb611fd45437f21c531848cf3e93b288bdc52494efc90ae` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs Missense variant Context-only references	Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) Original source ↗ Supplementary Table 9 row 53 and Supplementary Table 6 row 23, tool 'GERP++_RS_b', BRCA2 columns Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41436_2021_1265_MOESM3_ESM.xlsx Retrieved: 2026-10-09T21:18:15Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `02df1b0dbf916d598dd8278ba45091022bf78c5722ac13a07d5b1b70d64dc179` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-10-84341e0b121f · Record review: source checked

2 source records and release history

Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes · Original source · Genetics in Medicine 23(11):2096, published 2021-07-06; PMC8553612 full-text XML
Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) · Original source · 41436_2021_1265_MOESM3_ESM.xlsx

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Technical metadata and extraction receipts

Stable ID: brca-20261009-eval-cubuk2021-gerppp-rs-b-brca2

areas: dna-genomes
contexts: clinical_research
origin: independent_paper
protocol: brca-20261009-protocol-cubuk2021-brca2
version: Primary source as retrieved 2026-10-09
comparison: protocol id: brca-20261009-protocol-cubuk2021-brca2; dataset version: Not reported; split: Whole truth set; population: 187 of 188 BRCA2 truth-set variants with a deleterious or tolerated call; inputs: Missense variant; adaptation: Not reported; metric implementation: Binary call at the Supplementary Table 5 threshold; PLR = TPR/FPR and likelihood ratio for benignity = TNR/FNR (Supplementary Table 7); aggregation: Pooled over variants; budget: Not reported
source locator: Supplementary Table 9 row 53 and Supplementary Table 6 row 23, tool 'GERP++_RS_b', BRCA2 columns
missing metadata: comparison.dataset version: reason: unreported

Related records

system: GERP++_RS_b (Cubuk et al. 2021)
assessment: BRCA2 functional truth set, binary in silico calls (Cubuk et al. 2021)
data: BRCA2 functional truth set: 188 missense variants classed deleterious or tolerated by Homology-directed repair
evaluation: GERP++_RS_b BRCA2 likelihood ratio for benignity
evaluation: GERP++_RS_b BRCA2 false negatives
evaluation: GERP++_RS_b BRCA2 positive likelihood ratio

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