The effect of a single SMARCA4 exon deletion on RNA splicing: Implications for variant classification

BackgroundExon deletions are generally considered pathogenic, particularly when they are located out of frame. Here, we describe a pediatric, female patient presenting with hypercalcemia and a small cell carcinoma of the ovary, hypercalcemic type, and carrying a germline de novo SMARCA4 exon 14 deletion. MethodsThe SMARCA4 deletion was identified by whole genome sequencing, and the effect on the RNA level was examined by gel- and capillary electrophoresis and nanopore sequencing. ResultsThe deletion was in silico predicted to be truncating, but RNA analysis revealed two major transcripts with deletion of exon 14 alone or exon 14 through 15, where the latter was located in-frame. Because the patient's phenotype matched that of other patients with pathogenic germline variants in SMARCA4, the deletion was classified as likely pathogenic. ConclusionWe propose to include RNA analysis in classification of single-exon deletions, especially if located outside of known functional domains, as this can identify any disparate effects on the RNA and DNA level, which may have implications for variant classification using the American College of Medical Genetics and Genomics guidelines.

Automated summary

This study reports a new SMARCA4 deletion in a female patient with ovarian small cell carcinoma and hypercalcemia. The deletion was found to have different effects on the RNA level, highlighting the importance of incorporating RNA analysis in the classification of single-exon deletions.