The yield on re-interpretation of genetic variants in pediatric cardiomyopathy
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Background
Regular re-interpretation of disease-causing genetic variants is recommended to determine if variant pathogenicity changes as new information becomes available. Our aim was to determine the yield on systematic re-evaluation of genetic variants in pediatric patients with cardiomyopathy.
Methods
The study cohort included 227 unrelated pediatric patients with cardiomyopathy enrolled in the Heart Centre Biobank who harbored a pathogenic/likely pathogenic (P/LP) variant and/or a variant of uncertain significance (VUS) on clinical genetic testing between 2005-2022. Variant pathogenicity was re-evaluated using the American College of Medical Genetics and Genomics (ACMG) guidelines. The re-evaluation included updates to ClinGen gene curation, ClinVar variant interpretation, population allele frequency, in silico tools for variant deleteriousness, segregation with disease or de novo status, and genotype-phenotype evaluation.
Results
Re-evaluation was performed in 382 variants (110 P/LP, 272 VUS) reported in the study cohort of 227 patients. 12 of 110 P/LP (10.9%) variants were downgraded to VUS in 14 patients. Leading criteria were high population allele frequency and variant not located in mutational hotspot or critical functional gene domain. 37 of 272 VUS (13.6%) were upgraded to P/LP in 35 patients. Leading criteria were variant in mutational hotspot for gene, variant interpreted as deleterious using in silico prediction and novel missense change at an amino acid residue where a different missense change was previously determined to be pathogenic. Overall, the reclassification of 49 variants affected 49 of 227 (21.6%) patients. Of note, only 8 reclassified variants had been reported back by the clinical genetic testing laboratory.
Conclusions
One in five patients with cardiomyopathy had a clinically relevant change from the original variant classification on systematic re-evaluation. This has implications for clinical screening and cascade genetic testing of family members of affected patients. These findings underscore the importance of regular variant re-interpretation on follow-up in cardiomyopathy patients.
