P689: A multi-site study of constitutional ring chromosomes from 14 cytogenetics laboratories in the United States

explored how inclusion of ClinGen VCEP specifications affected variant reclassification frequencies in our clinical laboratory as compared to the 2015 ACMG/ AMP guidelines.Methods: We reviewed laboratory data of patients who underwent hereditary cancer panel genetic testing between January 2016 -October 2024 at the North York General Hospital Molecular Genetics Laboratory, Toronto, Ontario.Germline missense, synonymous, intronic, and frameshift/nonsense variants in BRCA1, BRCA2, ATM, CDH1, PALB2, and mismatch repair (MMR) genes (PMS2, MLH1, MSH2, and MSH6) were originally classified using the 2015 ACMG/AMP sequence variant guidelines.Following VCEP guideline inclusion, variants were seen for reinterpretation and included for analysis.Information relating to variant curation, including pathogenicity and classification codes applied, was collected and compared before vs after inclusion of VCEP specifications.Results: Of the 4095 unique variants detected in our laboratory, 208 were seen for reclassification using VCEP specifications (95 BRCA1/2, 60 ATM, 13 CDH1, 22 PALB2, and 18 in MMR genes) within the study period.Overall, 26.4% of variants (55/208) were re-classified to a different category using VCEP specifications: 5.3% (11/208) were upgraded in pathogenicity, while 21.2% (44/208) were downgraded.Most classification changes occurred in VUS, with 38.3% (44/115) of VUS reclassified into a meaningful category (41 LB/B; 3 LP/P).Only one variant, ATM c.6154G>A, was downgraded from a meaningful category (LP) to VUS due to published functional and co-segregation studies no longer meeting VCEP specification code criteria.The BRCA1/2 VCEP specifications resulted in the greatest number of meaningful classification changes for VUS, with 69.4% (25/36) of VUS upgraded or downgraded (3 LP/P, 22 B/LB).The most common reason for downgrade was the use of BP1_Strong, which was applicable in 41.7% (15/36) of BRCA1/2 VUS.Notably, all LP variants in BRCA1/2 were upgraded to pathogenic: 3 frameshift/nonsense variants were upgraded due to the applicability of PM5_PTC, and 1 missense variant was upgraded due to the use of PP4_VeryStrong for multifactorial likelihood clinical data.The CDH1 VCEP specifications resulted in the second largest number of VUS reclassifications, with 66.6% (8/12) of VUS reclassified into a meaningful category (all were downgraded to LB/B).Applicability of the BS2 code was the most common reason for classification changes in CDH1.Conclusion: By adopting VCEP specifications for variant curation in our clinical laboratory, we achieved an overall 26.4% variant reclassification frequency, with 38.3% of VUS reclassified into a meaningful category that increased or decreased their clinical significance.The BRCA1/2 VCEP resulted in the most drastic reclassification frequency, demonstrating the utility of this VCEP in addressing ambiguous calls.Our results support VCEP specification implementation in clinical settings, which may help reduce VUS calls and ultimately result in more clinically meaningful findings for clinicians and patients.Further studies with larger cohorts are needed to explore the clinical utility and cost-effectiveness of incorporating gene-disease specific guidelines.Ultimately, these guidelines may help standardize variant curation across clinical laboratories, leading to more effective and accurate curations.