Reclassification of Genetic Variants in Patients with Hypertrophic Cardiomyopathy from the Sarcomeric Human Cardiomyopathy Registry (SHaRe)
Hespe, S.; Powell, G.; Catto, L.; Stewart, N.; Baker, A.; Krishnan, N.; Mitchell, L. A.; Henden, N.; Richardson, E.; Butters, A.; Theotokis, P.; Buchan, R.; McGurk, K. A.; Claggett, B.; Abrams, D.; Ashley, E.; Parikh, V. N.; Day, S. M.; Helms, A. S.; Lampert, R.; Lin, K. Y.; Rossano, J. W.; Zwetsloot, P. P.; Michels, M.; Miller, E. M.; Girolami, F.; Olivotto, I.; Owens, A.; Pereira, A. C.; Ryan, T. D.; Saberi, S.; Russell, M. W.; Stendahl, J. C.; Gray, B.; Argiro, A.; Maurizi, N.; Crotti, L.; Vissing, C. R.; Lakdawala, N. K.; Ho, C. Y.; Ware, J. S.; Ingles, J.
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Background: Genetic testing is a Class I recommendation for patients with hypertrophic cardiomyopathy (HCM). As knowledge and frameworks continue to evolve, genetic variant classifications may change with new evidence over time. Classifications rely on evidence sought from publicly available case data, improved classification rules, and gene-disease validity. We evaluated the frequency and reasons for variant reclassification from a large multi-center international HCM registry (Sarcomeric Human Cardiomyopathy Registry; SHaRe). Methods: Participants were clinically evaluated at specialised HCM centres. Genetic variants were sought from the genetic test report, with classifications based on either the initial report, an updated report or some underwent further SHaRe adjudication. All variants were computationally reannotated and reevaluated. Variants underwent expedited curation if no new evidence was present. The remainder underwent full manual curation using accepted criteria and classified as pathogenic/likely pathogenic (P/LP), variant of uncertain significance (VUS) and benign/likely benign (B/LB). Results: Of 12,187 HCM patients, 8,054 (66%) had genetic testing between 1989-2020, and 4,923 (61%) had a variant identified in one of 29 HCM genes (1606 unique variants). Expedited curation was performed for 704 (44%) variants and 902 (56%) underwent manual curation. There were 1275 (79%) variants that retained their classification: 146 B/LB, 660 VUS, and 468 P/LP. While 276 (17%) variants (n=672 patients) were reclassified (n=276), including 73 upgrades: 61 from VUS to P/LP (199 patients), and 12 from B/LB to VUS. There were 203 downgrades: 108 from P/LP to VUS (n=196 patients), and 95 from P/LP or VUS to B/LB. VUS were additionally subclassified: 90 VUS-High, 129 VUS-Mid, 115 VUS-Low. Sub-classification of VUS resulted in less uncertainty, with 369 (40.6%) variants reclassified as VUS-Low or B/LB, indicating a very strong probability of not being HCM associated. Conclusions: Clinically meaningful reclassification occurred in 10% of variants identified in HCM probands. Most VUS were unlikely to be causal, and sub-classification has potential to reduce their burden on clinicians and families. Periodic reevaluation is essential for accurate clinical interpretation.
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