| Configuration: LRT (Cubuk et al. 2021) | Protocol: BRCA1 functional truth set, binary in silico calls (Cubuk et al. 2021)
Dataset: BRCA1 functional truth set: 1641 missense variants classed deleterious or tolerated by HAP1 cell survival after saturation genome editing | 2.99 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (2.70-3.30) 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 checkedMethods, coverage and sourceLRT on the BRCA1 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca1 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'), G25; tool 'LRT'; column 'BRCA1_negative_LR' |
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| Configuration: LRT (Cubuk et al. 2021) | Protocol: BRCA1 functional truth set, binary in silico calls (Cubuk et al. 2021)
Dataset: BRCA1 functional truth set: 1641 missense variants classed deleterious or tolerated by HAP1 cell survival after saturation genome editing | 85 false-negative-count count · lower Uncertainty: Not applicable: Count Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLRT on the BRCA1 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca1 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'), L28; tool 'LRT'; column 'BRCA1_FN' |
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| Configuration: LRT (Cubuk et al. 2021) | Protocol: BRCA1 functional truth set, binary in silico calls (Cubuk et al. 2021)
Dataset: BRCA1 functional truth set: 1641 missense variants classed deleterious or tolerated by HAP1 cell survival after saturation genome editing | 2.46 likelihood-ratio unitless · higher Uncertainty: CI 2.22 to 2.71. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLRT on the BRCA1 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca1 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'), F25; tool 'LRT'; column 'BRCA1_positive_LR' |
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| Configuration: LRT (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 | 9.62 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (8.50-10.8) 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 checkedMethods, coverage and sourceLRT 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'), I25; tool 'LRT'; column 'BRCA2_negative_LR' |
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| Configuration: LRT (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 checkedMethods, coverage and sourceLRT 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'), U28; tool 'LRT'; column 'BRCA2_FN' |
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| Configuration: LRT (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 | 1.38 likelihood-ratio unitless · higher Uncertainty: CI 1.22 to 1.56. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLRT 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'), H25; tool 'LRT'; column 'BRCA2_positive_LR' |
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