VUS

A variant of uncertain significance (VUS) is a genetic change identified during sequencing where there is insufficient evidence to classify it as either pathogenic (disease-causing) or benign (harmless). VUS are the clinical bottleneck in genomic medicine.

ACMG Classification System

The American College of Medical Genetics and Genomics (ACMG) defines five variant classification tiers:

1. Pathogenic — causes disease
2. Likely pathogenic — probably causes disease
3. VUS — uncertain significance
4. Likely benign — probably harmless
5. Benign — harmless

Why VUS Are a Problem

As pharmacogenomic and cancer genetic testing expands, novel rare variants appear constantly. Most haven’t been characterized experimentally, so they land in the VUS category. Clinicians need to act on incomplete information — a patient’s warfarin dose, cancer risk, or treatment choice may depend on whether a CYP2C9 or BRCA1 variant is damaging.

Computational Evidence (PP3/BP4)

ACMG criteria PP3 (pathogenic) and BP4 (benign) allow computational variant predictions to contribute to reclassification. Tools like REVEL, AlphaMissense, and ESM-2 provide this evidence. Alone, computational evidence is typically insufficient to reclassify a VUS — but combined with functional data, population data, and co-segregation evidence, it contributes to the overall classification.

ESM-2 and VUS

ESM-2’s masked marginal scores provide provisional PP3/BP4 evidence for missense VUS while functional testing is pending. All scores should be designated Research Use Only (RUO) — clinical laboratories validate computational tools as part of their own laboratory-developed test (LDT) workflows.