Evaluation

BayesDel ≥0.28, BRCA1 MAVE LoF discrimination (Ramadane-Morchadi et al. 2025)

Published in silico evidence comparison for BRCA1/BRCA2 missense variants; transcribed, not reproduced.

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Evaluation results

1 evaluation · 5 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, BP4 ≤0.15 and PP3 ≥0.28 (Ramadane-Morchadi et al. 2025)	Protocol: BRCA1 MAVE LoF discrimination at the PP3 threshold (Ramadane-Morchadi et al. 2025 Table 2) Dataset: BRCA1 RING and BRCT missense variants with saturation genome editing functional class (Findlay et al. 2018), LoF versus FUNC	85.6% accuracy percent · higher Uncertainty: 95% CI 83.7 to 87.3 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel ≥0.28, BRCA1 MAVE LoF discrimination (Ramadane-Morchadi et al. 2025) brca-20261009-protocol-ramadane2025-binary Aggregation: Not reported ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence · Table 2, 'BD' group, row '≥0.28', column 'Accuracy'
Configuration: BayesDel, BP4 ≤0.15 and PP3 ≥0.28 (Ramadane-Morchadi et al. 2025)	Protocol: BRCA1 MAVE LoF discrimination at the PP3 threshold (Ramadane-Morchadi et al. 2025 Table 2) Dataset: BRCA1 RING and BRCT missense variants with saturation genome editing functional class (Findlay et al. 2018), LoF versus FUNC	93.8% negative-predictive-value percent · higher Uncertainty: 95% CI 92.5 to 94.9 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel ≥0.28, BRCA1 MAVE LoF discrimination (Ramadane-Morchadi et al. 2025) brca-20261009-protocol-ramadane2025-binary Aggregation: Not reported ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence · Table 2, 'BD' group, row '≥0.28', column 'NPV'
Configuration: BayesDel, BP4 ≤0.15 and PP3 ≥0.28 (Ramadane-Morchadi et al. 2025)	Protocol: BRCA1 MAVE LoF discrimination at the PP3 threshold (Ramadane-Morchadi et al. 2025 Table 2) Dataset: BRCA1 RING and BRCT missense variants with saturation genome editing functional class (Findlay et al. 2018), LoF versus FUNC	64.1% precision percent · higher Uncertainty: 95% CI 60.3 to 67.6 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel ≥0.28, BRCA1 MAVE LoF discrimination (Ramadane-Morchadi et al. 2025) brca-20261009-protocol-ramadane2025-binary Aggregation: Not reported ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence · Table 2, 'BD' group, row '≥0.28', column 'PPV'
Configuration: BayesDel, BP4 ≤0.15 and PP3 ≥0.28 (Ramadane-Morchadi et al. 2025)	Protocol: BRCA1 MAVE LoF discrimination at the PP3 threshold (Ramadane-Morchadi et al. 2025 Table 2) Dataset: BRCA1 RING and BRCT missense variants with saturation genome editing functional class (Findlay et al. 2018), LoF versus FUNC	79.8% recall percent · higher Uncertainty: 95% CI 75.1 to 84.0 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel ≥0.28, BRCA1 MAVE LoF discrimination (Ramadane-Morchadi et al. 2025) brca-20261009-protocol-ramadane2025-binary Aggregation: Not reported ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence · Table 2, 'BD' group, row '≥0.28', column 'Sensitivity'
Configuration: BayesDel, BP4 ≤0.15 and PP3 ≥0.28 (Ramadane-Morchadi et al. 2025)	Protocol: BRCA1 MAVE LoF discrimination at the PP3 threshold (Ramadane-Morchadi et al. 2025 Table 2) Dataset: BRCA1 RING and BRCT missense variants with saturation genome editing functional class (Findlay et al. 2018), LoF versus FUNC	87.2% specificity percent · higher Uncertainty: 95% CI 85.2 to 89.1 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BayesDel ≥0.28, BRCA1 MAVE LoF discrimination (Ramadane-Morchadi et al. 2025) brca-20261009-protocol-ramadane2025-binary Aggregation: Not reported ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence · Table 2, 'BD' group, row '≥0.28', column 'Specificity'

Source checking is not independent reproduction. Release 2026-10-10-84341e0b121f.

Evaluation procedure

brca-20261009-protocol-ramadane2025-binary

Configuration: BayesDel, BP4 ≤0.15 and PP3 ≥0.28 (Ramadane-Morchadi et al. 2025)
Protocol: BRCA1 MAVE LoF discrimination at the PP3 threshold (Ramadane-Morchadi et al. 2025 Table 2)
Dataset: BRCA1 RING and BRCT missense variants with saturation genome editing functional class (Findlay et al. 2018), LoF versus FUNC

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-09
protocol id: brca-20261009-protocol-ramadane2025-binary
dataset version: Not reported
split: Whole dataset
population: 1,519 BRCA1 RING and BRCT missense variants: 337 LoF and 1,182 FUNC by MAVE score; 119 intermediate variants excluded
inputs: Missense variant (and structure for ΔΔG)
adaptation: Binary call at the PP3 threshold ≥0.28 only
metric implementation: Sensitivity, specificity, PPV, NPV and accuracy with 95% CI (MedCalc)
aggregation: Pooled over variants
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Whole dataset
Adaptation: Binary call at the PP3 threshold ≥0.28 only
Scoring implementation: Sensitivity, specificity, PPV, NPV and accuracy with 95% CI (MedCalc)

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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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

18 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.comparison.adaptation Binary call at the PP3 threshold ≥0.28 only Context-only references	ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence Original source ↗ Table 2, 'BD' group, row '≥0.28' Version: American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML Retrieved: 2026-10-09T21:18:06Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation Pooled over variants Context-only references	ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence Original source ↗ Table 2, 'BD' group, row '≥0.28' Version: American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML Retrieved: 2026-10-09T21:18:06Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence Original source ↗ Table 2, 'BD' group, row '≥0.28' Version: American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML Retrieved: 2026-10-09T21:18:06Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version Not reported Context-only references	ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence Original source ↗ Table 2, 'BD' group, row '≥0.28' Version: American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML Retrieved: 2026-10-09T21:18:06Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs Missense variant (and structure for ΔΔG) Context-only references	ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence Original source ↗ Table 2, 'BD' group, row '≥0.28' Version: American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML Retrieved: 2026-10-09T21:18:06Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.metric_implementation Sensitivity, specificity, PPV, NPV and accuracy with 95% CI (MedCalc) Context-only references	ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence Original source ↗ Table 2, 'BD' group, row '≥0.28' Version: American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML Retrieved: 2026-10-09T21:18:06Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.population 1,519 BRCA1 RING and BRCT missense variants: 337 LoF and 1,182 FUNC by MAVE score; 119 intermediate variants excluded Context-only references	ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence Original source ↗ Table 2, 'BD' group, row '≥0.28' Version: American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML Retrieved: 2026-10-09T21:18:06Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.protocol_id brca-20261009-protocol-ramadane2025-binary Context-only references	ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence Original source ↗ Table 2, 'BD' group, row '≥0.28' Version: American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML Retrieved: 2026-10-09T21:18:06Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.split Whole dataset Context-only references	ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence Original source ↗ Table 2, 'BD' group, row '≥0.28' Version: American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML Retrieved: 2026-10-09T21:18:06Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.origin independent_paper Context-only references	ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence Original source ↗ Table 2, 'BD' group, row '≥0.28' Version: American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML Retrieved: 2026-10-09T21:18:06Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.origin` Source artifact SHA-256: `cd089e7c621818f457f54f93c37cc1b9d535e531212b1aaf431fcbdd733bbda1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-10-84341e0b121f · Record review: source checked

1 source records and release history

ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence · Original source · American Journal of Human Genetics 112(5):993, published 2025; PMC12120176 full-text XML

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Technical metadata and extraction receipts

Stable ID: brca-20261009-eval-ramadane2025-bayesdel-0-15-0-28-binary

areas: dna-genomes
contexts: clinical_research
origin: independent_paper
protocol: brca-20261009-protocol-ramadane2025-binary
version: Primary source as retrieved 2026-10-09
comparison: protocol id: brca-20261009-protocol-ramadane2025-binary; dataset version: Not reported; split: Whole dataset; population: 1,519 BRCA1 RING and BRCT missense variants: 337 LoF and 1,182 FUNC by MAVE score; 119 intermediate variants excluded; inputs: Missense variant (and structure for ΔΔG); adaptation: Binary call at the PP3 threshold ≥0.28 only; metric implementation: Sensitivity, specificity, PPV, NPV and accuracy with 95% CI (MedCalc); aggregation: Pooled over variants; budget: Not reported
source locator: Table 2, 'BD' group, row '≥0.28'
missing metadata: comparison.dataset version: reason: unreported

Related records

system: BayesDel, BP4 ≤0.15 and PP3 ≥0.28 (Ramadane-Morchadi et al. 2025)
assessment: BRCA1 MAVE LoF discrimination at the PP3 threshold (Ramadane-Morchadi et al. 2025 Table 2)
data: BRCA1 RING and BRCT missense variants with saturation genome editing functional class (Findlay et al. 2018), LoF versus FUNC
evaluation: BayesDel ≥0.28 Accuracy
evaluation: BayesDel ≥0.28 NPV
evaluation: BayesDel ≥0.28 PPV
evaluation: BayesDel ≥0.28 Sensitivity
evaluation: BayesDel ≥0.28 Specificity

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