Whole exome sequencing (WES) captures all protein-coding regions (~1% of the genome). A clinical WES report identifies a variant of uncertain significance (VUS) in the BRCA2 gene. Which additional evidence is MOST useful for reclassifying this VUS as pathogenic?

• A The variant is found in dbSNP with a minor allele frequency (MAF) of 0.5%, making it a common polymorphism
• B The variant is located in an intronic region of BRCA2 unrelated to splicing
• C The patient has a positive ER receptor status on her breast tumor biopsy
• D The variant co-segregates with breast cancer across multiple generations of the family AND functional assay shows impaired BRCA2 homologous recombination activity ✓

Explanation

VUS classification uses multiple lines of evidence per ACMG/AMP guidelines. Co-segregation with disease across multiple affected family members provides strong evidence (PM1/PP1 criteria). A functional assay demonstrating impaired BRCA2 activity (homologous recombination repair) provides PS3-level evidence (well-established functional studies showing deleterious effect). Together, multiple lines of evidence can reclassify a VUS as likely pathogenic or pathogenic. A high MAF would argue for benign status. Intronic location remote from splicing sites suggests benign. Tumor receptor status is a separate molecular pathology finding unrelated to VUS classification.

Reference: Harper's Illustrated Biochemistry, 32nd ed.

High-yield for: NEET PGINI-CETNExTFMGEUSMLEPLABMRCP

Written and medically reviewed by the StethoPrep medical team.