Dataset

BRCA2 functional truth set: 188 missense variants classed deleterious or tolerated by Homology-directed repair

BRCA2 missense variants with a functional class, as assembled by Cubuk et al. 2021.

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These checks assess whether the evidence supports a reproducible investigation. A source-checked score alone does not meet these requirements.

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

Evidence incomplete

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Verified: Not verified

Evidence incomplete

Investigate discrepancies

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annotations: verification is missing
dependence: verification is missing

Verified: Not verified

Evidence incomplete

Run locally

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Missing or unresolved evidence

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Verified: Not verified

Evidence incomplete

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Separate data and exposure records support an independent test.

Missing or unresolved evidence

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artifact hashes: verification is missing
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score semantics: verification is missing
independent validation: verification is missing
overlap checked: verification is missing

Verified: Not verified

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Read reviewed discrepancy investigations

Evaluation results

84 evaluations · 226 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: alignGVGD_a (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	4.66 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (3.77-5.77) 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 alignGVGD_a 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'), I10; tool 'alignGVGD_a'; column 'BRCA2_negative_LR'
Configuration: alignGVGD_a (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	6 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 alignGVGD_a 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'), U2; tool 'alignGVGD_a'; column 'BRCA2_FN'
Configuration: alignGVGD_a (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	1.78 likelihood-ratio unitless · higher Uncertainty: CI 1.44 to 2.20. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source alignGVGD_a 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'), H10; tool 'alignGVGD_a'; column 'BRCA2_positive_LR'
Configuration: alignGVGD_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	4.03 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (3.24-5.01) 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 alignGVGD_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'), I11; tool 'alignGVGD_b'; column 'BRCA2_negative_LR'
Configuration: alignGVGD_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	8 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 alignGVGD_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'), U3; tool 'alignGVGD_b'; column 'BRCA2_FN'
Configuration: alignGVGD_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	1.87 likelihood-ratio unitless · higher Uncertainty: CI 1.50 to 2.33. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source alignGVGD_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'), H11; tool 'alignGVGD_b'; column 'BRCA2_positive_LR'
Configuration: BayesDEL_MaxAF_genespecific (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	0 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 BayesDEL_MaxAF_genespecific 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'), U4; tool 'BayesDEL_MaxAF_genespecific'; column 'BRCA2_FN'
Configuration: BayesDEL_MaxAF_genespecific (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	1.14 likelihood-ratio unitless · higher Uncertainty: CI 1.07 to 1.23. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDEL_MaxAF_genespecific 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'), H50; tool 'BayesDEL_MaxAF_genespecific'; column 'BRCA2_positive_LR'
Configuration: BayesDEL_MaxAF_universal (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	0 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 BayesDEL_MaxAF_universal 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'), U5; tool 'BayesDEL_MaxAF_universal'; column 'BRCA2_FN'
Configuration: BayesDEL_MaxAF_universal (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	1.51 likelihood-ratio unitless · higher Uncertainty: CI 1.33 to 1.72. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDEL_MaxAF_universal 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'), H52; tool 'BayesDEL_MaxAF_universal'; column 'BRCA2_positive_LR'
Configuration: BayesDEL_NoMaxAF_genespecific (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	0 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 BayesDEL_NoMaxAF_genespecific 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'), U6; tool 'BayesDEL_NoMaxAF_genespecific'; column 'BRCA2_FN'
Configuration: BayesDEL_NoMaxAF_genespecific (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 likelihood-ratio unitless · higher Uncertainty: CI 0.992 to 1.02. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDEL_NoMaxAF_genespecific 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'), H37; tool 'BayesDEL_NoMaxAF_genespecific'; column 'BRCA2_positive_LR'
Configuration: BayesDEL_NoMaxAF_universal (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	16.1 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (14.4-17.9) 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 BayesDEL_NoMaxAF_universal 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'), I38; tool 'BayesDEL_NoMaxAF_universal'; column 'BRCA2_negative_LR'
Configuration: BayesDEL_NoMaxAF_universal (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 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 BayesDEL_NoMaxAF_universal 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'), U7; tool 'BayesDEL_NoMaxAF_universal'; column 'BRCA2_FN'
Configuration: BayesDEL_NoMaxAF_universal (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	1.31 likelihood-ratio unitless · higher Uncertainty: CI 1.18 to 1.46. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDEL_NoMaxAF_universal 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'), H38; tool 'BayesDEL_NoMaxAF_universal'; column 'BRCA2_positive_LR'
Configuration: CADD_phred_a (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	0 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 CADD_phred_a 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'), U8; tool 'CADD_phred_a'; column 'BRCA2_FN'
Configuration: CADD_phred_a (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	1.07 likelihood-ratio unitless · higher Uncertainty: CI 1.02 to 1.13. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD_phred_a 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'), H47; tool 'CADD_phred_a'; column 'BRCA2_positive_LR'
Configuration: CADD_phred_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	0 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 CADD_phred_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'), U9; tool 'CADD_phred_b'; column 'BRCA2_FN'
Configuration: CADD_phred_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	1.02 likelihood-ratio unitless · higher Uncertainty: CI 0.996 to 1.05. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD_phred_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'), H60; tool 'CADD_phred_b'; column 'BRCA2_positive_LR'
Configuration: CHASM (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	0 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 CHASM 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'), U10; tool 'CHASM'; column 'BRCA2_FN'
Configuration: CHASM (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 likelihood-ratio unitless · higher Uncertainty: CI 1 to 1. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CHASM 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'), H64; tool 'CHASM'; column 'BRCA2_positive_LR'
Configuration: ClinPred (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	0 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 ClinPred 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'), U11; tool 'ClinPred'; column 'BRCA2_FN'
Configuration: ClinPred (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	1.46 likelihood-ratio unitless · higher Uncertainty: CI 1.29 to 1.65. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ClinPred 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'), H30; tool 'ClinPred'; column 'BRCA2_positive_LR'
Configuration: Concordant calls of PANTHER and MetaSNP (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	0 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 Combined-PANTHER-AND-MetaSNP 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'), U72; tool 'Combined-PANTHER-AND-MetaSNP'; column 'BRCA2_FN'
Configuration: Concordant calls of PANTHER and MetaSNP (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	1.65 likelihood-ratio unitless · higher Uncertainty: CI 1.36 to 2.01. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Combined-PANTHER-AND-MetaSNP 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'), H81; tool 'Combined-PANTHER-AND-MetaSNP'; column 'BRCA2_positive_LR'

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

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.

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14 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.assay Homology-directed repair (DR-GFP) assay of BRCA2 cDNA constructs in BRCA2-deficient V-C8 cells (Guidugli et al. 2014 and 2018; Richardson et al. 2021) 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 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' 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 Audit details Field: `attributes.assay` Source artifact SHA-256: `ea6391e04f5f01353bb611fd45437f21c531848cf3e93b288bdc52494efc90ae` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.assay Homology-directed repair (DR-GFP) assay of BRCA2 cDNA constructs in BRCA2-deficient V-C8 cells (Guidugli et al. 2014 and 2018; Richardson et al. 2021) Context-only references	Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) Original source ↗ Supplementary Table 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' 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 Audit details Field: `attributes.assay` Source artifact SHA-256: `02df1b0dbf916d598dd8278ba45091022bf78c5722ac13a07d5b1b70d64dc179` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.denominator 188 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 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' 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 Audit details Field: `attributes.denominator` Source artifact SHA-256: `ea6391e04f5f01353bb611fd45437f21c531848cf3e93b288bdc52494efc90ae` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.denominator 188 Context-only references	Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) Original source ↗ Supplementary Table 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' 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 Audit details Field: `attributes.denominator` Source artifact SHA-256: `02df1b0dbf916d598dd8278ba45091022bf78c5722ac13a07d5b1b70d64dc179` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.population 188 missense variants (64 deleterious, 124 tolerated) in DNA-binding domain (amino acids 2481-3186), 252 assayed missense variants; start gain or loss, nonsense, splice-region flanking and intermediate or conflicting variants excluded 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 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' 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 Audit details Field: `attributes.population` Source artifact SHA-256: `ea6391e04f5f01353bb611fd45437f21c531848cf3e93b288bdc52494efc90ae` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.population 188 missense variants (64 deleterious, 124 tolerated) in DNA-binding domain (amino acids 2481-3186), 252 assayed missense variants; start gain or loss, nonsense, splice-region flanking and intermediate or conflicting variants excluded Context-only references	Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) Original source ↗ Supplementary Table 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' 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 Audit details Field: `attributes.population` Source artifact SHA-256: `02df1b0dbf916d598dd8278ba45091022bf78c5722ac13a07d5b1b70d64dc179` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.source_locator Supplementary Table 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' 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 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' 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 Audit details Field: `attributes.source_locator` Source artifact SHA-256: `ea6391e04f5f01353bb611fd45437f21c531848cf3e93b288bdc52494efc90ae` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.source_locator Supplementary Table 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' Context-only references	Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) Original source ↗ Supplementary Table 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' 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 Audit details Field: `attributes.source_locator` Source artifact SHA-256: `02df1b0dbf916d598dd8278ba45091022bf78c5722ac13a07d5b1b70d64dc179` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.split Whole truth set; no training 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 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' 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 Audit details Field: `attributes.split` Source artifact SHA-256: `ea6391e04f5f01353bb611fd45437f21c531848cf3e93b288bdc52494efc90ae` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.split Whole truth set; no training Context-only references	Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) Original source ↗ Supplementary Table 2 and Supplementary Table 3; Methods 'Generation of functional truth sets' 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 Audit details Field: `attributes.split` Source artifact SHA-256: `02df1b0dbf916d598dd8278ba45091022bf78c5722ac13a07d5b1b70d64dc179` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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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-data-cubuk2021-brca2-functional

areas: dna-genomes
contexts: clinical_research
population: 188 missense variants (64 deleterious, 124 tolerated) in DNA-binding domain (amino acids 2481-3186), 252 assayed missense variants; start gain or loss, nonsense, splice-region flanking and intermediate or conflicting variants excluded
assay: Homology-directed repair (DR-GFP) assay of BRCA2 cDNA constructs in BRCA2-deficient V-C8 cells (Guidugli et al. 2014 and 2018; Richardson et al. 2021)
split: Whole truth set; no training
denominator: 188
source locator: Supplementary Table 2 and Supplementary Table 3; Methods 'Generation of functional truth sets'
missing metadata: version: reason: unreported; note: Assay data release not stated

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