Variant Classification of a Non-Protein Coding Gene: ACMG/AMP Specifications for RMRP from the Clinical Genome Resource Severe Combined Immunodeficiency Disease Variant Curation Expert Panel

Abstract

PurposeThis study, conducted by the Clinical Genome Resource Severe Combined Immunodeficiency Disease Variant Curation Expert Panel (ClinGen SCID-VCEP), aimed to adapt the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) framework for germline variant interpretation in RMRP. Unlike the protein-coding genes for which the framework was primarily developed, RMRP encodes a non-protein-coding RNA. Biallelic pathogenic variants in RMRP cause cartilage-hair hypoplasia, which can include severe combined immunodeficiency disease and other immune abnormalities. MethodsAn RMRP-focused SCID-VCEP subgroup reviewed all 28 ACMG/AMP evidence criteria using population databases, published clinical and experimental data, computational predictions, and expert consensus. Each criterion was retained, modified, or designated as not applicable based on RMRP biology and disease mechanisms. The resulting specifications were pilot tested using 27 variants selected from ClinVar and research laboratory data. ResultsFifteen ACMG/AMP criteria were determined to be applicable to RMRP, while 13 were considered not applicable. Several criteria were modified to evaluate nucleotide-level effects on transcriptional regulation, critical promoter regions, and RNA secondary structure. The specifications also incorporated RMRP-specific recommendations for population frequency, functional evidence, variant phase, segregation, and phenotype. Application of the specifications classified 6 variants as pathogenic, 10 as likely pathogenic, 7 as variants of uncertain significance, and 4 as benign. Previously pathogenic or likely pathogenic variants remained within the pathogenic spectrum, and all previously benign variants remained benign. Variants with conflicting ClinVar interpretations were resolved as either likely pathogenic or uncertain. PM1, PM3, and PP4 were the primary criteria supporting pathogenic classifications. ConclusionThe SCID-VCEP specifications provide a standardized approach to the classification of germline RMRP variants in cartilage-hair hypoplasia and demonstrate how the ACMG/AMP framework can be adapted for a disease-associated non-protein-coding RNA gene. These specifications support the development of variant interpretation frameworks for other clinically relevant non-protein-coding genes.