Configuration

AlphaMissense, BP4 ≤0.60 and PP3 ≥0.80 (Ramadane-Morchadi et al. 2025)

AlphaMissense with three-category PP3/BP4 thresholds.

Overview

AlphaMissense with three-category PP3/BP4 thresholds.

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Evaluations and results

1 evaluation · 3 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaMissense, BP4 ≤0.60 and PP3 ≥0.80 (Ramadane-Morchadi et al. 2025)	Protocol: BRCA1 MAVE PP3/BP4 evidence strength by score threshold (Ramadane-Morchadi et al. 2025 Table 1) Dataset: BRCA1 RING and BRCT missense variants with saturation genome editing functional class (Findlay et al. 2018), LoF versus FUNC	−3.038 log2-likelihood-ratio unitless · lower Uncertainty: 95% CI -3.508 to -2.569 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense, BP4 ≤0.60 and PP3 ≥0.80, BRCA1 MAVE evidence strength (Ramadane-Morchadi et al. 2025) brca-20261009-protocol-ramadane2025-pp3-bp4 Aggregation: Not reported ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence · Table 1, row 4 ('AM' group), column 'Benignity evidence (BP4): Evidence strength, log 2 LR (95% CI)'
Configuration: AlphaMissense, BP4 ≤0.60 and PP3 ≥0.80 (Ramadane-Morchadi et al. 2025)	Protocol: BRCA1 MAVE PP3/BP4 evidence strength by score threshold (Ramadane-Morchadi et al. 2025 Table 1) Dataset: BRCA1 RING and BRCT missense variants with saturation genome editing functional class (Findlay et al. 2018), LoF versus FUNC	10% proportion percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense, BP4 ≤0.60 and PP3 ≥0.80, BRCA1 MAVE evidence strength (Ramadane-Morchadi et al. 2025) brca-20261009-protocol-ramadane2025-pp3-bp4 Aggregation: Not reported ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence · Table 1, row 4 ('AM' group), column 'No bioinformatic code applicable'
Configuration: AlphaMissense, BP4 ≤0.60 and PP3 ≥0.80 (Ramadane-Morchadi et al. 2025)	Protocol: BRCA1 MAVE PP3/BP4 evidence strength by score threshold (Ramadane-Morchadi et al. 2025 Table 1) Dataset: BRCA1 RING and BRCT missense variants with saturation genome editing functional class (Findlay et al. 2018), LoF versus FUNC	3.01 log2-likelihood-ratio unitless · higher Uncertainty: 95% CI 2.746 to 3.269 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense, BP4 ≤0.60 and PP3 ≥0.80, BRCA1 MAVE evidence strength (Ramadane-Morchadi et al. 2025) brca-20261009-protocol-ramadane2025-pp3-bp4 Aggregation: Not reported ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence · Table 1, row 4 ('AM' group), column 'Pathogenicity evidence (PP3): Evidence strength, log 2 LR (95% CI)'

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Sources and history

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

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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-config-ramadane2025-am-0-60-0-80

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: AlphaMissense
foundation model eligible: false
protocol: BP4 if score ≤0.60, PP3 if score ≥0.80, no computational code in between
source locator: Table 1; Material and methods paragraphs 2-4
missing metadata: version: reason: unreported; note: Pre-computed scores from the dm_alphamissense storage bucket

Related records

configuration of: AlphaMissense
system: AlphaMissense, BP4 ≤0.60 and PP3 ≥0.80, BRCA1 MAVE evidence strength (Ramadane-Morchadi et al. 2025)

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