Protocol

BRCA1 BayesDel evidence calibration

Gene-specific three-category BayesDel likelihood ratios against functional reference labels, not held-out classification accuracy. Category thresholds were selected on this calibration set.

1 evaluation · 15 results

Overview

Gene-specific three-category BayesDel likelihood ratios against functional reference labels, not held-out classification accuracy. Category thresholds were selected on this calibration set.

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

1 recorded evaluation, 15 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

1 evaluation · 15 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: 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

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Benchmarks

ENIGMA 2024 BRCA evidence-calibration and curation study

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

BRCA1 BayesDel gene-specific calibration

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 1

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Training-set class prior where supervised fitting is permitted

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Regularised classifier on simple permitted features, or protocol's conventional reference

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-30-e37e3ab1284d. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Applicable tests and references

Applicability is distinct from a completed evaluation.

Gene-specific manual BRCA review baseline · source_supported

Evidence

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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.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-30-e37e3ab1284d
Property and statement	Original source and location	Review and provenance
Relationship: part of uc-clinical-20260930-benchmark-enigma-study 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 ↗ Table2; calibration Results; pilot curation Version: 2024 final article; reported VCEP specifications v1.0 Retrieved: 2026-09-30T21:24:15Z	source checked automated source review · 2026-09-30 Audit details Transcription from inspected primary source. No execution, independent replication or human scientific review. Field: `links:part_of:uc-clinical-20260930-benchmark-enigma-study` Claim: uc-clinical-20260930-membership-enigma-brca1-protocol Source artifact SHA-256: `21e7b0792e18a1295b7bccb8b19ebe4432a2b047187139407c8616ea0cd531f2` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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

1 source records 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-enigma-brca1-protocol

areas: dna-genomes
contexts: clinical_research
protocol: Gene-specific three-category BayesDel likelihood ratios against functional reference labels, not held-out classification accuracy. Category thresholds were selected on this calibration set.
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
limitations: Calibration, not independent held-out validation.; Functional labels are proxy pathogenicity classes.; Clinical reviewer effort and serious final-classification error are not measured.; Full score variant and training overlap not established.

Related records

part of: ENIGMA 2024 BRCA evidence-calibration and curation study
applicable to: Gene-specific manual BRCA review baseline
protocol: BRCA1 BayesDel gene-specific calibration
subject: Published study membership: BRCA1 BayesDel evidence calibration

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