Evaluating the Impact of ClinGen Variant Curation Expert Panel Criteria Specifications on Variant Interpretation...

Gene-specific variant interpretation guidelines are constantly being published to refine variant classification. The development, implementation, and benefit of such guidelines require careful assessment. This study evaluates the utility of these guidelines on variant interpretation. All actionable genes listed in American College of Medical Genetics and Genomics-Secondary findings version 3.3 genes with available Clinical Genome Resource (ClinGen) Variant Curation Expert Panel criteria specifications were analyzed. A total of 1223 variants in these genes were classified using the American College of Medical Genetics and Genomics/Association for Molecular Pathology criteria and revised according to the Variant Curation Expert Panel specifications. Reclassification outcomes were compared using high-confidence variants. Application of the revised guidelines resulted in score changes in 63.1% of variants, although most did not cross classification thresholds. Reclassification occurred in 20.3% of cases, predominantly as downgrades and improved concordance with ClinVar by 5.8%, particularly for benign classifications. Of 622 variants of uncertain significance (VUSs), 25.1% were resolved, with the highest resolution rates in BRCA1, BRCA2, and PALB2, whereas LDLR and TPM1 remained largely unchanged. No consistent correlation was found between the extent of criteria modification for each guideline and VUS resolution. The utility of the guidelines was shown to be variable and gene dependent. Although most reduced VUS rates and refined benign classifications, in some, only a minor impact was achieved, suggesting standardization and calibration of future guidelines are necessary.