Clinical Utility of a Phenotype-Enhanced MYH7-Specific Variant Classification Framework in Hypertrophic Cardiomyopathy Genetic Testing.

BACKGROUND: Missense variants in the MYH7-encoded MYH7 (beta myosin heavy chain 7) represent a leading cause of hypertrophic cardiomyopathy (HCM). MYH7-specific American College of Medical Genetics and Genomics (ACMG) variant classification guidelines were released recently but have yet to be assessed independently. We set out to assess the performance of the MYH7-specific ACMG guidelines and determine if the addition of phenotype-enhanced criteria (PE-ACMG) using the HCM Genotype Predictor Score can further reduce the burden of variants of uncertain significance (VUS). METHODS: Re-assessment was performed on 70 MYH7-variants in 121 unique patients from Mayo Clinic, and an independent cohort of 54 variants in 70 patients from Royal Prince Alfred Hospital (Australia). Qualifying variants were re-adjudicated using both standard ACMG and MYH7-ACMG guidelines, and HCM Genotype Predictor Score was used to provide a validated measure of strength of clinical phenotype to be incorporated into the MYH7-ACMG framework. RESULTS: Among Mayo Clinic identified variants, 11/70 (16%) were classified as pathogenic (P), 10/70 (14%) as likely pathogenic, and 49/70 (70%) as a VUS. A similar distribution was seen in the Australian patients (12/54 [22%] P, 12/54 [22%] likely pathogenic, and 30/54 [56%] VUS; P=not significant). Application of the MYH7-ACMG resulted in a nonsignificant reduction of the VUS burden in both cohorts from 49/70 to 39/70 (56%; P=0.1; Mayo Clinic) and from 30/54 to 20/54 (37%; P=0.1; Australia). Using the combined PE-MYH7-ACMG framework, the VUS decreased significantly from 49 to 27 (P<0.001, Mayo Clinic) and from 30 to 16 (P<0.001; Australia). CONCLUSIONS: Use of the MYH7-specific guidelines alone failed to significantly decrease VUS burden in 2 independent cohorts. However, a significant reduction in VUS burden was observed after the addition of phenotypic criteria. Using a patient's strength of sarcomeric HCM phenotype for variant adjudication can increase significantly the clinical utility of genetic testing for patients with HCM.

Utilization of the genome aggregation database, in silico tools, and heterologous expression patch-clamp studies to identify and demote previously published type 2 long QT syndrome: Causative variants from pathogenic to likely benign.

BACKGROUND: Loss-of-function variants in the KCNH2-encoded Kv11.1 potassium channel cause long QT syndrome (LQTS) type 2 (LQT2). Presently, hundreds of KCNH2 missense variants (MVs) have been published as "disease-causative." However, an estimated 10% of rare published LQTS MVs may be "false positives." OBJECTIVE: The purpose of this study was to determine which published KCNH2 MVs are likely false positives and warrant demotion to "likely benign" status. METHODS: A list of 337 LQT2-associated MVs from 6 large compendia was compiled. MV frequency within the Genome Aggregation Database (gnomAD) (n = 141,352 individuals) was assessed, and MVs were analyzed with 8 in silico tools. Variants with minor allele frequency (MAF) >7*10E-6, the calculated maximum credible frequency of LQT2, and predicted "benign" by all tools were demoted to "likely benign." Ultra-rare variants (n = 8) absent in gnomAD but predicted "benign" by all tools were considered as potential false positives and were characterized functionally using whole-cell patch clamp. RESULTS: Overall, 14 of 337 published KCNH2 MVs (4%) were observed at MAF >7*10E-6, whereas 252 of 337 (75%) were absent in gnomAD. Among the latter, 8 variants (I96V, G187S, A203T, P241L, H254Q, G314S, P935S, P963T) were predicted benign by 8 tools and lacked characterization. Patch clamp showed no functional perturbation for these 8 MVs. CONCLUSION: This study offers compelling evidence for the demotion of 22 of 337 KCNH2 variants (6.5%) in the literature. Meticulous "pruning" of compendia using exome/genome databases, in silico tools, and in vitro functional studies must be conducted not only for putatively pathogenic LQTS MVs but for the entire field of genetic heart disease.