Evaluation

phyloP20way_mammalian 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: phyloP20way_mammalian (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	2.16 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (1.65-2.83) 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 phyloP20way_mammalian 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'), I45; tool 'phyloP20way_mammalian'; column 'BRCA2_negative_LR'
Configuration: phyloP20way_mammalian (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	18 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 phyloP20way_mammalian 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'), U51; tool 'phyloP20way_mammalian'; column 'BRCA2_FN'
Configuration: phyloP20way_mammalian (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	1.84 likelihood-ratio unitless · higher Uncertainty: CI 1.40 to 2.40. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phyloP20way_mammalian 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'), H45; tool 'phyloP20way_mammalian'; column 'BRCA2_positive_LR'

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

Evaluation procedure

brca-20261009-protocol-cubuk2021-brca2

Configuration: phyloP20way_mammalian (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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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

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 45 and Supplementary Table 6 row 51, tool 'phyloP20way_mammalian', 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 45 and Supplementary Table 6 row 51, tool 'phyloP20way_mammalian', 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 45 and Supplementary Table 6 row 51, tool 'phyloP20way_mammalian', 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 45 and Supplementary Table 6 row 51, tool 'phyloP20way_mammalian', 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 45 and Supplementary Table 6 row 51, tool 'phyloP20way_mammalian', 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 45 and Supplementary Table 6 row 51, tool 'phyloP20way_mammalian', 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 45 and Supplementary Table 6 row 51, tool 'phyloP20way_mammalian', 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 45 and Supplementary Table 6 row 51, tool 'phyloP20way_mammalian', 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 45 and Supplementary Table 6 row 51, tool 'phyloP20way_mammalian', 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 45 and Supplementary Table 6 row 51, tool 'phyloP20way_mammalian', 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-phylop20way-mammalian-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 45 and Supplementary Table 6 row 51, tool 'phyloP20way_mammalian', BRCA2 columns
missing metadata: comparison.dataset version: reason: unreported

Related records

system: phyloP20way_mammalian (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: phyloP20way_mammalian BRCA2 likelihood ratio for benignity
evaluation: phyloP20way_mammalian BRCA2 false negatives
evaluation: phyloP20way_mammalian BRCA2 positive likelihood ratio

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