Modeling the ACMG/AMP Variant Classification Guidelines as a Bayesian Classification Framework

Abstract

Purpose

We evaluated the ACMG/AMP variant pathogenicity guidelines for internal consistency and compatibility with Bayesian statistical reasoning.

Methods

The ACMG/AMP criteria were translated into a naïve Bayesian classifier, assuming four levels of evidence and exponentially scaled odds of pathogenicity. We tested this framework with a range of prior probabilities and odds of pathogenicity.

Results

We modeled the ACMG/AMP guidelines using biologically plausible assumptions. Most ACMG/AMP combining criteria were compatible. One ACMG/AMP likely pathogenic combination was mathematically equivalent to pathogenic and one ACMG/AMP pathogenic combination was actually likely pathogenic. We modeled combinations that include evidence for and against pathogenicity, showing that our approach scored some combinations as pathogenic or likely pathogenic that ACMG/AMP would designate as VUS.

Conclusion

By transforming the ACMG/AMP guidelines into a Bayesian framework, we provide a mathematical foundation for what was a qualitative heuristic. Only two of the 18 existing ACMG/AMP evidence combinations were mathematically inconsistent with the overall framework. Mixed combinations of pathogenic and benign evidence could yield a likely pathogenic, likely benign, or VUS result. This quantitative framework validates the approach adopted by the ACMG/AMP, provides opportunities to further refine evidence categories and combining rules, and supports efforts to automate components of variant pathogenicity assessments.