The Clinical Genome Resource (ClinGen) Familial Hypercholesterolemia Variant Curation Expert Panel consensus guidelines for LDLR variant classification

Abstract

PurposeIn 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published consensus standardized guidelines for variant classification in Mendelian disorders. To increase accuracy and consistency, the Clinical Genome Resource (ClinGen) Familial Hypercholesterolemia (FH) Variant Curation Expert Panel (VCEP) was tasked with optimizing the existing ACMG/AMP framework for disease-specific classification in FH. Here, we provide consensus recommendations for the most common FH-causing gene, LDLR, where >2,300 unique FH-associated variants have been identified. MethodsThe multidisciplinary FH VCEP met in person and through frequent emails and conference calls to develop LDLR-specific modifications of ACMG/AMP guidelines. Through iteration, pilot testing, debate and commentary, consensus among experts was reached. ResultsThe consensus LDLR variant modifications to existing ACMG/AMP guidelines include: 1) alteration of population frequency thresholds; 2) delineation of loss-of-function variant types; 3) functional study criteria specifications; 4) co-segregation criteria specifications; and 5) specific use and thresholds for in silico prediction tools, among others. ConclusionEstablishment of these guidelines as the new standard in the clinical laboratory setting will result in a more evidence-based, harmonized method for LDLR variant classification worldwide, thereby improving the care of FH patients.