Dataset

BRCA1 functional truth set: 1641 missense variants classed deleterious or tolerated by HAP1 cell survival after saturation genome editing

BRCA1 missense variants with a functional class, as assembled by Cubuk et al. 2021.

Research readiness

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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score semantics: verification is missing
metric replay: verification is missing

Verified: Not verified

Evidence incomplete

Investigate discrepancies

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Missing or unresolved evidence

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artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
metric replay: verification is missing
annotations: verification is missing
dependence: verification is missing

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
recipe pinned: verification is missing
resource estimate: verification is missing

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
independent validation: verification is missing
overlap checked: verification is missing

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Read reviewed discrepancy investigations

Evaluation results

84 evaluations · 247 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: alignGVGD_a (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	2.61 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (2.14-3.17) 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 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'), G10; tool 'alignGVGD_a'; column 'BRCA1_negative_LR'
Configuration: alignGVGD_a (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	105 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 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'), L2; tool 'alignGVGD_a'; column 'BRCA1_FN'
Configuration: alignGVGD_a (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	7.05 likelihood-ratio unitless · higher Uncertainty: CI 5.79 to 8.59. 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 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'), F10; tool 'alignGVGD_a'; column 'BRCA1_positive_LR'
Configuration: alignGVGD_b (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	2.44 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (2.02-2.96) 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 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'), G11; tool 'alignGVGD_b'; column 'BRCA1_negative_LR'
Configuration: alignGVGD_b (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	125 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 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'), L3; tool 'alignGVGD_b'; column 'BRCA1_FN'
Configuration: alignGVGD_b (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	6.67 likelihood-ratio unitless · higher Uncertainty: CI 5.51 to 8.08. 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 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'), F11; tool 'alignGVGD_b'; column 'BRCA1_positive_LR'
Configuration: BayesDEL_MaxAF_genespecific (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	17.2 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (16.9-17.5) 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_MaxAF_genespecific 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'), G50; tool 'BayesDEL_MaxAF_genespecific'; column 'BRCA1_negative_LR'
Configuration: BayesDEL_MaxAF_genespecific (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 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 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'), L4; tool 'BayesDEL_MaxAF_genespecific'; column 'BRCA1_FN'
Configuration: BayesDEL_MaxAF_genespecific (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	1.09 likelihood-ratio unitless · higher Uncertainty: CI 1.07 to 1.11. 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 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'), F50; tool 'BayesDEL_MaxAF_genespecific'; column 'BRCA1_positive_LR'
Configuration: BayesDEL_MaxAF_universal (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	15.9 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (15.6-16.2) 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_MaxAF_universal 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'), G52; tool 'BayesDEL_MaxAF_universal'; column 'BRCA1_negative_LR'
Configuration: BayesDEL_MaxAF_universal (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 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 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'), L5; tool 'BayesDEL_MaxAF_universal'; column 'BRCA1_FN'
Configuration: BayesDEL_MaxAF_universal (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	1.08 likelihood-ratio unitless · higher Uncertainty: CI 1.06 to 1.10. 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 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'), F52; tool 'BayesDEL_MaxAF_universal'; column 'BRCA1_positive_LR'
Configuration: BayesDEL_NoMaxAF_genespecific (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	10.8 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (10.4-11.1) 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_genespecific 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'), G37; tool 'BayesDEL_NoMaxAF_genespecific'; column 'BRCA1_negative_LR'
Configuration: BayesDEL_NoMaxAF_genespecific (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	7 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 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'), L6; tool 'BayesDEL_NoMaxAF_genespecific'; column 'BRCA1_FN'
Configuration: BayesDEL_NoMaxAF_genespecific (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	1.23 likelihood-ratio unitless · higher Uncertainty: CI 1.19 to 1.27. 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 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'), F37; tool 'BayesDEL_NoMaxAF_genespecific'; column 'BRCA1_positive_LR'
Configuration: BayesDEL_NoMaxAF_universal (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	11.8 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (11.5-12.2) 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 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'), G38; tool 'BayesDEL_NoMaxAF_universal'; column 'BRCA1_negative_LR'
Configuration: BayesDEL_NoMaxAF_universal (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	7 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 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'), L7; tool 'BayesDEL_NoMaxAF_universal'; column 'BRCA1_FN'
Configuration: BayesDEL_NoMaxAF_universal (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	1.26 likelihood-ratio unitless · higher Uncertainty: CI 1.22 to 1.30. 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 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'), F38; tool 'BayesDEL_NoMaxAF_universal'; column 'BRCA1_positive_LR'
Configuration: CADD_phred_a (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	36.7 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (36.0-37.4) 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 CADD_phred_a 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'), G47; tool 'CADD_phred_a'; column 'BRCA1_negative_LR'
Configuration: CADD_phred_a (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	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 CADD_phred_a 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'), L8; tool 'CADD_phred_a'; column 'BRCA1_FN'
Configuration: CADD_phred_a (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	1.1 likelihood-ratio unitless · higher Uncertainty: CI 1.08 to 1.12. 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 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'), F47; tool 'CADD_phred_a'; column 'BRCA1_positive_LR'
Configuration: CADD_phred_b (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	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 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'), L9; tool 'CADD_phred_b'; column 'BRCA1_FN'
Configuration: CADD_phred_b (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	1.03 likelihood-ratio unitless · higher Uncertainty: CI 1.02 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 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'), F60; tool 'CADD_phred_b'; column 'BRCA1_positive_LR'
Configuration: CHASM (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	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 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'), L10; tool 'CHASM'; column 'BRCA1_FN'
Configuration: CHASM (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	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 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'), F64; tool 'CHASM'; column 'BRCA1_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

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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 HAP1 cell survival after saturation genome editing (Findlay et al. 2018) 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 HAP1 cell survival after saturation genome editing (Findlay et al. 2018) 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 1641 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 1641 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 1641 missense variants (371 deleterious, 1270 tolerated) in 13 exons covering the RING and BRCT domains; 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 1641 missense variants (371 deleterious, 1270 tolerated) in 13 exons covering the RING and BRCT domains; 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

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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-brca1-functional

areas: dna-genomes
contexts: clinical_research
population: 1641 missense variants (371 deleterious, 1270 tolerated) in 13 exons covering the RING and BRCT domains; start gain or loss, nonsense, splice-region flanking and intermediate or conflicting variants excluded
assay: HAP1 cell survival after saturation genome editing (Findlay et al. 2018)
split: Whole truth set; no training
denominator: 1641
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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