Enhancing Variant Curation Guidelines to Optimize Clinical Genetic Testing for ABCA4 Retinopathies Utilizing the ClinGen Framework

Abstract

Purpose : Genetic testing for ABCA4-related retinopathies is a diagnostic tool that aids in risk stratification, family planning and is a prerequisite for delivering potentially sight preserving gene therapy in the future. Currently in ClinVar, there are 240 variants with conflicting classifications and 816 variants of uncertain significance (VUS). Therefore, disambiguation of VUS to increase the variant classification accuracy in public databases, like ClinVar and Leiden Open Variation Database (LOVD), is critically important.

Methods : The Clinical Genome Resource (ClinGen), funded by the National Human Genome Research Institute, convened the ABCA4 Variant Curation Expert Panel (VCEP) in June 2022 to develop rule specifications for curating variants through their FDA-approved process. The 2015 American College of Medical Genetics and Association for Molecular Pathology (ACMG/AMP) variant curation framework was used to specify rule codes for the ABCA4 gene along with rules previously developed for the ABCA4-LOVD database.

The ABCA4 VCEP members meet monthly to specify ACMG-AMP rules to enhance resulting variant assertions. Each rule was assessed for its appropriateness for the ABCA4 gene and whether there would be any benefit to adding detailed criteria for its use and/or modifying its strength based on availability of evidence.

Results : Variant curation specifications were applied to 16 individual ACMG-AMP rule criteria and 12 rules were deemed not applicable to ABCA4-related retinopathy. Criteria modifications included setting allele frequencies in unaffected controls, defining phenotype criteria and conditions for adjusting rule strength from a supporting to very strong weight. A set of ~45 ABCA4 variants were chosen for a pilot study testing the rule specifications; this included 15 pathogenic/likely pathogenic, 15 VUS and 15 benign/likely benign variants.

Conclusions : Results of this effort will aid clinical variant interpretation of the ABCA4 gene and standardize variant curations across databases, literature and clinical laboratories. Expert level variant curation from this VCEP will be deposited in the ClinVar database for public access and variant classifications will be updated over time.

This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.