ACMG Variant Classification Assistant v3.0.0

Release Date: July 9, 2025

Summary

Version 3.0.0 completes the implementation of all 28 ACMG/AMP evidence criteria as specified in the 2015 and 2023 guidelines.

Implementation Status

Pathogenic Evidence Criteria (16/16)

• PVS1: Null variants in loss-of-function intolerant genes
• PS1: Same amino acid change as established pathogenic variant
• PS2: De novo occurrence in patient with disorder and no family history
• PS3: Well-established in vitro or in vivo functional studies
• PS4: Case-control studies showing increased prevalence in affected individuals
• PM1: Located in mutational hot spot or critical functional domain
• PM2: Absent from controls or at extremely low frequency
• PM3: For recessive disorders, detected in trans with pathogenic variant
• PM4: Protein length changes as result of in-frame deletions/insertions
• PM5: Novel missense change at amino acid residue where different missense change is pathogenic
• PM6: Assumed de novo, but without confirmation of paternity and maternity
• PP1: Cosegregation with disease in multiple affected family members
• PP2: Missense variant in gene that has low rate of benign missense variation
• PP3: Multiple lines of computational evidence support deleterious effect
• PP4: Patient's phenotype or family history highly specific for gene
• PP5: Reputable source recently reports variant as pathogenic

Benign Evidence Criteria (12/12)

• BA1: Allele frequency >5% in population databases
• BS1: Allele frequency greater than expected for disorder
• BS2: Observed in healthy adult individual for recessive disorder
• BS3: Well-established in vitro or in vivo functional studies show no effect
• BS4: Lack of segregation in affected members of family
• BP1: Missense variant in gene for which primarily truncating variants cause disease
• BP2: Observed in trans with pathogenic variant for fully penetrant dominant gene
• BP3: In-frame deletions/insertions in repetitive region without known function
• BP4: Multiple lines of computational evidence suggest no impact
• BP5: Variant found in case with alternate molecular basis for disease
• BP6: Reputable source recently reports variant as benign
• BP7: Synonymous variant for which splicing prediction algorithms predict no impact

Technical Changes

Evidence Evaluation System

• Centralized evaluation logic in EvidenceEvaluator class
• Interactive user input for criteria requiring literature review (PS1, PS4, PM3, PM5, PP4, BP2, BP5, BP6)
• Automated assessment for data-driven criteria (population frequencies, computational predictions)
• Test mode support for non-interactive validation

Computational Framework

• Enhanced metascore calculation using multiple prediction algorithms
• Population frequency analysis with gene-specific thresholds
• SpliceAI integration for splice impact assessment
• Conservation score analysis across multiple species

Code Structure

• Modular architecture with separate modules for each functional area
• Comprehensive input validation and error handling
• Enhanced reporting system with detailed evidence breakdown
• Test suite covering all implemented criteria

References

Implementation follows ACMG/AMP variant interpretation guidelines:

• Richards et al. (2015) Genetics in Medicine 17:405-424
• ClinGen SVI working group updates (2023)