Method

BayesDel

Computational variant-effect scoring method; study applies gene-specific evidence calibration.

Overview

Computational variant-effect scoring method; study applies gene-specific evidence calibration.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

4 evaluations · 34 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: BayesDel generic Pejaver evidence thresholds in ENIGMA comparison	Protocol: BRCA1 generic BayesDel threshold evidence-code assignment Dataset: BRCA1 functional reference calibration set	<10% benign_reference_assigned_bp4 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 generic BayesDel threshold comparator Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Results, BayesDel calibration, BP4 code would be assigned to <10% of BRCA1 and BRCA2 benign reference variants
Configuration: BayesDel generic Pejaver evidence thresholds in ENIGMA comparison	Protocol: BRCA1 generic BayesDel threshold evidence-code assignment Dataset: BRCA1 functional reference calibration set	29% benign_reference_assigned_pp3 percent · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 generic BayesDel threshold comparator Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Results, BayesDel calibration, sentence 29% for BRCA1 and 36% for BRCA2 incorrectly assigned PP3
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	149 high_benign_count count · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel ≥0.28, benign_count
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	12% high_benign_fraction percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel ≥0.28, benign_fraction
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	7.09 high_likelihood_ratio likelihood ratio · unknown Uncertainty: type: confidence_interval; level: 0.95; lower: 6.06; upper: 8.30; printed: 6.06–8.30 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel ≥0.28, likelihood_ratio
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	377 high_pathogenic_count count · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel ≥0.28, pathogenic_count
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	83% high_pathogenic_fraction percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel ≥0.28, pathogenic_fraction
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	946 low_benign_count count · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel ≤0.15, benign_count
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	74% low_benign_fraction percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel ≤0.15, benign_fraction
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	0.1 low_likelihood_ratio likelihood ratio · unknown Uncertainty: type: confidence_interval; level: 0.95; lower: 0.07; upper: 0.14; printed: 0.07–0.14 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel ≤0.15, likelihood_ratio
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	34 low_pathogenic_count count · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel ≤0.15, pathogenic_count
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	7% low_pathogenic_fraction percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel ≤0.15, pathogenic_fraction
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	183 middle_benign_count count · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel >0.15 and <0.28, benign_count
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	14% middle_benign_fraction percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel >0.15 and <0.28, benign_fraction
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	0.69 middle_likelihood_ratio likelihood ratio · unknown Uncertainty: type: confidence_interval; level: 0.95; lower: 0.51; upper: 0.94; printed: 0.51–0.94 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel >0.15 and <0.28, likelihood_ratio
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	45 middle_pathogenic_count count · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel >0.15 and <0.28, pathogenic_count
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA1 BayesDel evidence calibration Dataset: BRCA1 functional reference calibration set	10% middle_pathogenic_fraction percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA1 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA1, BayesDel >0.15 and <0.28, pathogenic_fraction
Configuration: BayesDel generic Pejaver evidence thresholds in ENIGMA comparison	Protocol: BRCA2 generic BayesDel threshold evidence-code assignment Dataset: BRCA2 functional reference calibration set	<10% benign_reference_assigned_bp4 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA2 generic BayesDel threshold comparator Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Results, BayesDel calibration, BP4 code would be assigned to <10% of BRCA1 and BRCA2 benign reference variants
Configuration: BayesDel generic Pejaver evidence thresholds in ENIGMA comparison	Protocol: BRCA2 generic BayesDel threshold evidence-code assignment Dataset: BRCA2 functional reference calibration set	36% benign_reference_assigned_pp3 percent · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA2 generic BayesDel threshold comparator Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Results, BayesDel calibration, sentence 29% for BRCA1 and 36% for BRCA2 incorrectly assigned PP3
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA2 BayesDel evidence calibration Dataset: BRCA2 functional reference calibration set	29 high_benign_count count · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA2 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA2, BayesDel ≥0.30, benign_count
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA2 BayesDel evidence calibration Dataset: BRCA2 functional reference calibration set	10% high_benign_fraction percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA2 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA2, BayesDel ≥0.30, benign_fraction
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA2 BayesDel evidence calibration Dataset: BRCA2 functional reference calibration set	6.59 high_likelihood_ratio likelihood ratio · unknown Uncertainty: type: confidence_interval; level: 0.95; lower: 4.40; upper: 9.90; printed: 4.40–9.90 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA2 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA2, BayesDel ≥0.30, likelihood_ratio
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA2 BayesDel evidence calibration Dataset: BRCA2 functional reference calibration set	88 high_pathogenic_count count · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA2 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA2, BayesDel ≥0.30, pathogenic_count
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA2 BayesDel evidence calibration Dataset: BRCA2 functional reference calibration set	66% high_pathogenic_fraction percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA2 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA2, BayesDel ≥0.30, pathogenic_fraction
Configuration: BayesDel with ENIGMA BRCA gene-specific score categories	Protocol: BRCA2 BayesDel evidence calibration Dataset: BRCA2 functional reference calibration set	216 low_benign_count count · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BRCA2 BayesDel gene-specific calibration Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Table 2, BRCA2, BayesDel ≤0.18, benign_count

Source checking is not independent reproduction. Release 2026-09-30-e37e3ab1284d.

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Versions and evaluated configurations

BayesDel with ENIGMA BRCA gene-specific score categories · variant of
BayesDel generic Pejaver evidence thresholds in ENIGMA comparison · variant of

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Evidence

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Release 2026-09-30-e37e3ab1284d · Record review: source checked

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Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Original source · 2024 final article; reported VCEP specifications v1.0

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Technical metadata and extraction receipts

Stable ID: uc-clinical-20260930-method-bayesdel

areas: dna-genomes
contexts: clinical_research
source locator: Results; Table 2; reference 22
review: method: automated_source_review; reviewer: Codex clinical coverage worker; date: 2026-09-30; note: Transcription from inspected primary source. No execution, independent replication or human scientific review.; source id: uc-clinical-20260930-source-enigma

Related records

variant of: BayesDel with ENIGMA BRCA gene-specific score categories
variant of: BayesDel generic Pejaver evidence thresholds in ENIGMA comparison

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