Method

BayesDel

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

4 evaluations · 34 results 14 configurations with further results

Overview

An explanatory profile has not yet been reviewed for this record.

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.

Sorted by Proportion (benign reference variants assigned BP4) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Proportion (benign reference variants assigned BP4)	Proportion (benign reference variants assigned PP3)	Proportion (interval: high, benign)	Proportion (interval: high, pathogenic)	Proportion (interval: low, benign)	Proportion (interval: low, pathogenic)	Count (interval: high, benign)	Count (interval: high, pathogenic)	Count (interval: low, benign)	Count (interval: low, pathogenic)	Count (interval: middle, benign)	Count (interval: middle, pathogenic)	Likelihood ratio (interval: high)	Likelihood ratio (interval: low)	Likelihood ratio (interval: middle)	Proportion (interval: middle, benign)	Proportion (interval: middle, pathogenic)
BayesDel generic Pejaver evidence thresholds in ENIGMA comparisonEvaluation	BRCA1 generic BayesDel threshold evidence-code assignment, BRCA1 functional reference calibration set	<10%	29% (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
BayesDel with ENIGMA BRCA gene-specific score categoriesEvaluation	BRCA1 BayesDel evidence calibration, BRCA1 functional reference calibration set	Not reported	Not reported	12%	83% (best in column)	74% (best in column)	7% (best in column)	149	377	946	34	183	45	7.09	0.1	0.69	14%	10%
BayesDel generic Pejaver evidence thresholds in ENIGMA comparisonEvaluation	BRCA2 generic BayesDel threshold evidence-code assignment, BRCA2 functional reference calibration set	<10%	36%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
BayesDel with ENIGMA BRCA gene-specific score categoriesEvaluation	BRCA2 BayesDel evidence calibration, BRCA2 functional reference calibration set	Not reported	Not reported	10% (best in column)	66%	74% (best in column)	16%	29	88	216	21	46	25	6.59	0.21	1.18	16%	19%

All 34 result rows with coverage, uncertainty and sources

Filter evaluations

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: BayesDel generic Pejaver evidence thresholds in ENIGMA comparison	Protocol: BRCA1 generic BayesDel threshold evidence-code assignment Dataset: BRCA1 functional reference calibration set	<10% Proportion (benign reference variants assigned BP4) percent · higher Uncertainty: Not reported by the source: not reported for this endpoint 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% Proportion (benign reference variants assigned PP3) percent · lower Uncertainty: Not reported by the source: not reported for this endpoint 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 Count (interval: high, benign) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint 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% Proportion (interval: high, benign) percent · lower Uncertainty: Not reported by the source: not reported for this endpoint 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 Likelihood ratio (interval: high) unitless · unknown Uncertainty: 95% CI 6.06 to 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 Count (interval: high, pathogenic) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint 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% Proportion (interval: high, pathogenic) percent · higher Uncertainty: Not reported by the source: not reported for this endpoint 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 Count (interval: low, benign) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint 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% Proportion (interval: low, benign) percent · higher Uncertainty: Not reported by the source: not reported for this endpoint 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 Likelihood ratio (interval: low) unitless · unknown Uncertainty: 95% CI 0.07 to 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 Count (interval: low, pathogenic) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint 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% Proportion (interval: low, pathogenic) percent · lower Uncertainty: Not reported by the source: not reported for this endpoint 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 Count (interval: middle, benign) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint 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% Proportion (interval: middle, benign) percent · unknown Uncertainty: Not reported by the source: not reported for this endpoint 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 Likelihood ratio (interval: middle) unitless · unknown Uncertainty: 95% CI 0.51 to 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 Count (interval: middle, pathogenic) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint 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% Proportion (interval: middle, pathogenic) percent · unknown Uncertainty: Not reported by the source: not reported for this endpoint 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% Proportion (benign reference variants assigned BP4) percent · higher Uncertainty: Not reported by the source: not reported for this endpoint 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% Proportion (benign reference variants assigned PP3) percent · lower Uncertainty: Not reported by the source: not reported for this endpoint 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 Count (interval: high, benign) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint 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% Proportion (interval: high, benign) percent · lower Uncertainty: Not reported by the source: not reported for this endpoint 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 Likelihood ratio (interval: high) unitless · unknown Uncertainty: 95% CI 4.40 to 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 Count (interval: high, pathogenic) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint 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% Proportion (interval: high, pathogenic) percent · higher Uncertainty: Not reported by the source: not reported for this endpoint 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 Count (interval: low, benign) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint 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 2026-10-22-1b7cf027e4f6.

Further results on linked records

14 linked records have results that are not included above, because no reviewed claim yet ties the link to this method. Each record keeps its own settings and evaluations, and its scores are on its own page.

BayesDEL_MaxAF_genespecific (Cubuk et al. 2021) Configuration · configuration · 2 evaluations · 5 results
BayesDEL_MaxAF_universal (Cubuk et al. 2021) Configuration · configuration · 2 evaluations · 5 results
BayesDEL_NoMaxAF_genespecific (Cubuk et al. 2021) Configuration · configuration · 2 evaluations · 5 results
BayesDEL_NoMaxAF_universal (Cubuk et al. 2021) Configuration · configuration · 2 evaluations · 6 results
BayesDel, BP4 ≤0.15 and PP3 ≥0.28 (Ramadane-Morchadi et al. 2025) Configuration · configuration · 2 evaluations · 8 results
BayesDel (no AF) (Brandes et al. 2023 head-to-head comparison) Configuration · configuration · 2 evaluations · 4 results
BayesDel (with AF) (Brandes et al. 2023 head-to-head comparison) Configuration · configuration · 2 evaluations · 4 results
BayesDel_addAF rank score, dbNSFP 5.3.1a (Lee 2026) Configuration · configuration · 3 evaluations · 6 results
BayesDel_noAF rank score, dbNSFP 5.3.1a (Lee 2026) Configuration · configuration · 3 evaluations · 6 results
BayesDel (Livesey and Marsh 2025) Configuration · configuration · 6 evaluations · 7 results
BayesDel_noAF (Livesey and Marsh 2025) Configuration · configuration · 6 evaluations · 7 results
BayesDel (addAF) [ProteinGym 144fe22 clinical summary] Configuration · configuration · 1 evaluation · 1 result
BayesDel (noAF) [ProteinGym 144fe22 clinical summary] Configuration · configuration · 1 evaluation · 1 result
BayesDel (Pejaver et al. 2022 calibration) Configuration · configuration · 2 evaluations · 17 results

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How it works, versions and access

Versions and evaluated configurations

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

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Facets: method types 1 values supervised_machine_learning Individual claims	ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence Original source ↗ Matches the other 7 BayesDel configurations; Ramadane 2025 calls BayesDel a meta-predictor Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML Retrieved: 2026-10-09T21:18:06Z	conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit details Correct the method type from none to supervised_machine_learning (use-case baseline review 2026-10-12, table 2). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: `"[\"supervised_machine_learning\"]"`. Claim record status: source_checked. Field: `facets.method_types` Claim: metadata-correction-tags-20261012-fbd56a605d0c73b4a368 Source artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Extraction artifact
Facets: method types 1 values supervised_machine_learning Individual claims	Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel Original source ↗ Matches the other 7 BayesDel configurations; Ramadane 2025 calls BayesDel a meta-predictor Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2024 final article; reported VCEP specifications v1.0 Retrieved: 2026-09-30T21:24:15Z	conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit details Correct the method type from none to supervised_machine_learning (use-case baseline review 2026-10-12, table 2). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: `"[\"supervised_machine_learning\"]"`. Claim record status: source_checked. Field: `facets.method_types` Claim: metadata-correction-tags-20261012-fbd56a605d0c73b4a368 Source artifact SHA-256: `21e7b0792e18a1295b7bccb8b19ebe4432a2b047187139407c8616ea0cd531f2` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Extraction artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

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
method types: supervised_machine_learning
source locator: Results; Table 2; reference 22
review: method: automated-source-review; reviewer: codex; 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; reviewer note: role: clinical coverage worker

Related records

configuration of: BayesDEL_MaxAF_genespecific (Cubuk et al. 2021)
configuration of: BayesDEL_MaxAF_universal (Cubuk et al. 2021)
configuration of: BayesDEL_NoMaxAF_genespecific (Cubuk et al. 2021)
configuration of: BayesDEL_NoMaxAF_universal (Cubuk et al. 2021)
configuration of: BayesDel, BP4 ≤0.15 and PP3 ≥0.28 (Ramadane-Morchadi et al. 2025)
configuration of: BayesDel (no AF) (Brandes et al. 2023 head-to-head comparison)
configuration of: BayesDel (with AF) (Brandes et al. 2023 head-to-head comparison)
subject: BayesDel: facets.method_types
configuration of: BayesDel_addAF rank score, dbNSFP 5.3.1a (Lee 2026)
configuration of: BayesDel_noAF rank score, dbNSFP 5.3.1a (Lee 2026)
configuration of: BayesDel with ENIGMA BRCA gene-specific score categories
configuration of: BayesDel generic Pejaver evidence thresholds in ENIGMA comparison
configuration of: BayesDel (Livesey and Marsh 2025)
configuration of: BayesDel_noAF (Livesey and Marsh 2025)
configuration of: BayesDel (addAF) [ProteinGym 144fe22 clinical summary]
configuration of: BayesDel (noAF) [ProteinGym 144fe22 clinical summary]
configuration of: BayesDel (Pejaver et al. 2022 calibration)

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