| Configuration: PMut (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 | 5.93 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (5.45-6.45) 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 sourcePMut 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'), G4; tool 'PMut'; column 'BRCA1_negative_LR' |
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| Configuration: PMut (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 | 41 false-negative-count count · lower Uncertainty: Not applicable: Count Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcePMut 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'), L52; tool 'PMut'; column 'BRCA1_FN' |
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| Configuration: PMut (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 | 2.58 likelihood-ratio unitless · higher Uncertainty: CI 2.37 to 2.81. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcePMut 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'), F4; tool 'PMut'; column 'BRCA1_positive_LR' |
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| Configuration: PMut (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 | 3.94 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (2.48-6.25) 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 sourcePMut 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'), I4; tool 'PMut'; column 'BRCA2_negative_LR' |
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| Configuration: PMut (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 | 14 false-negative-count count · lower Uncertainty: Not applicable: Count Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcePMut 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'), U52; tool 'PMut'; column 'BRCA2_FN' |
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| Configuration: PMut (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 | 5.69 likelihood-ratio unitless · higher Uncertainty: CI 3.59 to 9.02. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcePMut 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'), H4; tool 'PMut'; column 'BRCA2_positive_LR' |
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