Reclassification of variants of uncertain significance in neonatal genetic diseases: implications from a clinician's perspective.

Abstract

Although whole-exome sequencing (WES) is now widely used to diagnose neonatal genetic diseases, the genetic causes in over half of the cases remain unresolved, primarily due to variants of uncertain significance (VUS). Therefore, reclassifying VUS may be an effective strategy to improve WES's diagnostic yield. However, not all reclassification approaches are suitable for clinicians. Patients in the neonatal unit of Hebei Provincial Children's Hospital who underwent WES for suspected genetic diseases and demonstrated VUS were re-evaluated from January 2019 to December 2023 using user-friendly methods. A total of 676 individuals were tested, with 101 phenotype-associated VUS identified in 82 patients. Thirty (29.7%) VUS classifications were changed: 24 were upgraded to likely pathogenic or pathogenic, and 6 were downgraded to likely benign. VUS reclassification clarified the molecular diagnosis in 19 cases, increasing the WES diagnostic rate from 30.2% to 33.0%. Computational prediction contributed the most to reclassification, whereas clinical phenotype-related evidence was also particularly significant in upgrading variants. Moreover, phenotype-associated VUS with a score of ≥3 points are more likely to be classified as likely pathogenic or pathogenic, thus requiring more attention. This study provides a practical reference for clinicians in managing VUS reclassification.