ACMG Assistant v3.4.0 Release Notes

Version 3.4.0 implements a configuration-based dual guidelines system supporting both ACMG/AMP 2015 and 2023 standards. This architecture allows users to select between guideline versions while maintaining backward compatibility with existing workflows.

Technical Changes

ACMG 2023 Guidelines Implementation

The following criteria have been updated to reflect ClinGen Sequence Variant Interpretation (SVI) Working Group 2023 recommendations:

PS4 - Case-Control Evidence

ACMG 2015 Requirements:

• Odds Ratio (OR) ≥ 2.0
• Minimum 5 affected probands
• Minimum 1,000 controls
• Statistical significance (p < 0.05)

ACMG 2023 Requirements:

• Odds Ratio (OR) ≥ 5.0
• Minimum 10 affected probands
• Minimum 2,000 controls
• Statistical significance (p < 0.05)

Rationale: Increased thresholds reduce false positive classifications from underpowered studies.

PP1 - Segregation Analysis

ACMG 2015:

• LOD score ≥ 3.0 applies PP1 at Moderate strength

ACMG 2023:

• LOD score 1.5-2.99: PP1_Supporting
• LOD score 3.0-4.99: PP1_Moderate
• LOD score ≥ 5.0: PP1_Strong

Rationale: Tiered strength assignment reflects statistical confidence levels in segregation data.

PS2 - De Novo Evidence

ACMG 2015:

• Confirmed de novo (maternity and paternity tested): PS2 (Strong)

ACMG 2023:

• Confirmed de novo (both parents tested): PS2_Very_Strong

Rationale: High confidence in de novo status when both parents are tested justifies strength upgrade.

PP5 - Reputable Source

ACMG 2023 Only:

• Available when --acmg-2023 flag is used
• Applies when variant reported as pathogenic by reputable sources without detailed evidence available for independent review

Architecture

Architecture

Configuration System

Threshold values for both guideline versions are stored in separate configuration dictionaries:

# config/constants.py
STATISTICAL_THRESHOLDS_2015 = {
    'case_control_odds_ratio': 2.0,
    'case_control_min_cases': 5,
    'case_control_min_controls': 1000,
    'segregation_lod_score': 3.0,
    'pm5_min_pathogenic_variants': 1
}

STATISTICAL_THRESHOLDS_2023 = {
    'case_control_odds_ratio': 5.0,
    'case_control_min_cases': 10,
    'case_control_min_controls': 2000,
    'segregation_lod_supporting': 1.5,
    'segregation_lod_moderate': 3.0,
    'segregation_lod_strong': 5.0,
    'pm5_min_pathogenic_variants': 2
}

# Default: ACMG 2015
STATISTICAL_THRESHOLDS = STATISTICAL_THRESHOLDS_2015

Evidence Evaluator

The EvidenceEvaluator class accepts a use_2023_guidelines boolean parameter that controls threshold selection:

# Version-aware initialization
evaluator = EvidenceEvaluator(use_2023_guidelines=False)  # ACMG 2015
evaluator = EvidenceEvaluator(use_2023_guidelines=True)   # ACMG 2023

Criteria evaluation methods dynamically select appropriate thresholds:

• _evaluate_ps4(): Selects OR and sample size thresholds based on version
• _evaluate_pp1(): Applies tiered strength modifiers in 2023 mode
• _evaluate_ps2(): Upgrades to Very Strong when applicable in 2023 mode
• _evaluate_pp5(): Only evaluates in 2023 mode

Bug Fixes

Classification Rules

Issue: Benign classification incorrectly applied with BS1 + 1 BP
Fix: Corrected classification rules to require BS1 + ≥2 BP for Benign classification
Impact: BS1 + BP4 now correctly classified as Likely Benign per ACMG 2015 standards

PP2 Criterion

Issue: Automatic application caused false positives in genes with low benign missense rates
Fix: Converted to interactive mode requiring user confirmation
Implementation:

• Test mode: Returns manual review flag with guidance
• Interactive mode: Prompts user with context-specific warnings
• Added frequency filter: Variants with gnomAD AF > 0.001 excluded

Test Expectations

Issue: Test cases expected "Likely Pathogenic" for variants meeting Pathogenic criteria
Fix: Aligned test expectations with ACMG Rule (iii): 1 Strong + ≥3 Moderate = Pathogenic
Example: PS1 + PM1 + PM2 + PM5 now correctly expected to classify as Pathogenic

Validation

Test Coverage

| Test Suite | Tests | Pass Rate | Status | |-------------|-------|-----------|---------| | ACMG 2015 Comprehensive | 30 | 100% | Validated | | ACMG 2023 Mode | 3 | 100% | Validated | | Total | 33 | 100% | Complete |

ACMG 2023 Test Scenarios

1. PS4 with high OR (6.5): Both 2015 and 2023 modes correctly apply PS4
2. PS4 with low OR (3.5): 2015 applies PS4, 2023 correctly rejects insufficient evidence
3. PP1 with LOD=5.5: 2015 applies at Moderate strength, 2023 upgrades to Strong

Changelog Summary

Added

• PP1 LOD-based strength modifiers (Supporting/Moderate/Strong)
• PS4 enhanced validation (OR≥5.0, sample size requirements)
• PS2 Very Strong upgrade capability
• PP5 criterion (ACMG 2023 only)
• Test suite for ACMG 2023 mode validation

Changed

• Evidence evaluator accepts use_2023_guidelines parameter
• PS4/PP1 criteria use version-specific thresholds
• Classification engine reports guidelines version in metadata

Fixed

• Benign classification rule (BS1 + ≥2 BP required)
• PP2 false positive rate (interactive mode implementation)
• Test case expectations aligned with ACMG standards

Removed

• Temporary diagnostic output files
• Obsolete documentation files

Known Limitations

1. PM5 threshold: Currently requires ≥1 pathogenic variant at same residue in 2015 mode, ≥2 in 2023 mode. Full implementation of PM5 2023 updates pending.

2. PVS1 pLI integration: Gene constraint scores (pLI) not yet integrated into PVS1 evaluation for 2023 mode.

3. PP4 phenotype specificity: Quantitative phenotype specificity scoring not yet implemented for 2023 mode.