A Retrospective Review of Reclassification of Variants of Uncertain Significance in a Pediatric Epilepsy Cohort Undergoing Genetic Panel Testing

Background

The interpretation and communication of variant of uncertain significance (VUS) genetic results often present a challenge in clinical practice. VUSs can be reclassified over time into benign/likely benign (B/LB) or pathogenic/likely pathogenic (P/LP) based on the availability of updated data. We evaluate the frequency of VUS reclassification in our tertiary care epilepsy cohort undergoing epilepsy genetic panel (EGP) testing.

Methods

Patients with established diagnoses of epilepsy (neonates to 18 years of age) who underwent EGP testing between 2017 and 2022 from a single commercial laboratory were evaluated. Patients who had any variant reclassified from their initial EGP report were included. Duration between reclassification of VUSs and types of reclassifications were compared between developmental and epileptic encephalopathy (DEE) versus non-DEE phenotypes.

Results

Over the five years, 1025 probands were tested using EGP. Eighty-five probands (8%) had at least one genetic variant reclassified. A total of 252 initial VUSs were reported in the 85 probands, of which 113 (45%) VUSs were reclassified. Of 113 reclassification events, 21 (19%) were upgraded to P/LP and 92 (81%) were reclassified to B/LB. The median (interquartile range) duration between variant reinterpretations in the cohort was 12 (14.5) months. There were no significant differences in the duration between reclassification and the likelihood of reclassification of VUSs to B/LB or P/LP between the two groups (DEE versus non-DEE).

Conclusions

VUS reclassification over time can lead to clinically significant variant reinterpretation in patients with unknown genetic diagnoses. Periodic genomic test reinterpretation, preferably yearly, is recommended in routine clinical practice.