Variant sub-tiering, disease-gene associations and strictness of clinical criteria improves the interpretation of variants of uncertain significance in hereditary cardiomyopathies and rhythm disorders

Abstract

Besides the ClinGen's efforts to standardize the ACMG/AMP criteria and European initiatives aimed at monitoring quality standards, molecular diagnostics of hereditary cardiomyopathies and heart rhythm disorders (HCHRDs) remains strongly influenced by the local strategies developed to overcome the variables in which genetic testing is requested. This is a monocentric study on the clinical and molecular findings of 363 pedigrees with various HCHRDs. ACMG/AMP criteria were adapted according to the ClinGen's material and internal specifications. Phenotypes were reviewed according to known disease-gene associations and the concurrence of multiple variants in the same individual. Relatives were studied when available and the significance of selected variants was supported by RNA- studies before reporting. One or more (likely) pathogenic variants were found in 80 pedigrees (22.0%), while 96 (26.4%) displayed one or more variants of uncertain significance (VUS) only. The 132 identified VUS were sub-tiered according to the Bayesian score in three categories presenting distinguishable patterns of selected criteria. VUS_high showed profiles of key molecular criteria and resembled deleterious variants according to the combinations of assigned criteria, while the VUS_low category displayed a high chance of conflicting combinations of criteria and unsupported disease-gene associations. Reclassification to likely pathogenic by the application of applicable clinical criteria (PVS1_Strength, PP1 and PP4) was accessible to VUS_high and a few VUS_mid only. This work supports the combined need to (i) introduce VUS sub-tiering, (ii) consider known disease-gene associations, (iii) stringently apply clinical criteria and (iv) incorporate RNA data to improve the clinical significance of genetic testing in HCHRDs.