Reclassification of VUS Using ACMG/AMP Criteria Adapted for Sarcomeric Genes Related to Hypertrophic Cardiomyopathy:...

Genetic testing is valuable to confirm molecular diagnosis in nearly 60% of cases suspected of hypertrophic cardiomyopathy (HCM). However, the interpretation of variants, especially those of uncertain significance (VUSs), remains challenging for laboratories and clinicians. In April 2024, the ClinGen Cardiomyopathy Variant Curation Expert Panel (VCEP) adapted the ACMG/AMP criteria for eight of the sarcomeric genes (MYH7, MYBPC3, TNNI3, TNNT2, TPM1, ACTC1, MYL2, and MYL3), providing a refined framework for variant interpretation in these genes. This retrospective study re-evaluated 69 VUSs identified in 84 HCM patients between 2017 and 2024, aiming to resolve uncertainty and reduce the VUS rate.

Here, two groups of curators reinterpreted variants with the most recent data using the Cardiomyopathy VCEP specifications until a consensus was reached. To streamline the process, we created a semiautomated decision support tool based on these gene-specific rules.

The application of the Cardiomyopathy VCEP specifications resulted in the reclassification of 17.4% (N = 12/69, 95% CI: 10.2%-28.0%) of VUS, whereas the new data alone were not sufficient. Out of the reclassified variants, 91.7% (N = 11/12) were downgraded to benignity (involving 17 patients), and 8.3% were upgraded to pathogenicity (involving one patient), with a mean reclassification time of 68.3 months, corresponding to 5.7 years. The most applied criteria were related to population (PM2 = 55%; BA1/BS1 = 16%), bioinformatic prediction (PP3 = 45%; BP4 = 25%), and critical domains (PM1 = 21%). However, most codes suffer from a lack of evidence (segregation data, functional assays, and case-control studies). When comparing this curation with classifications in public databases, 13.3% (N = 8/60) and 16.2% (N = 11/68) of variants listed as having inconclusive significance in ClinVar and CardioClassifier were, respectively, reclassified in this study.

Using gene-specific ACMG/AMP criteria reduces the rate of VUS, increasing diagnostic yield, and informing clinical management in the context of HCM. Nonetheless, ongoing efforts to generate evidence and promote standardization remain essential to improve variant interpretation.