Splicing Predictions, Splicing Assays, and Variant Classification Using ACMG/AMP Guidelines: Challenges Observed with BRCA1 and BRCA2 Variants

BRCA1, BRCA2 (splicing variants, VUS reclassification)

Combination of in silico prediction (SpliceAI, MaxEntScan) + functional splicing assays (mRNA) + ACMG/AMP classification with new ClinGen SVI Splicing Subgroup criteria (PVS1_RNA, BP7_S(RNA)) on a BRCA1/BRCA2 series; reclassification of 4 P/LP, 10 B/LB and 3 residual VUS

Study illustrating the application of new ClinGen SVI Splicing Subgroup criteria (PVS1_RNA, BP7_S(RNA)) to the classification of BRCA1/BRCA2 splicing variants. Among evaluated variants, 4 are classified P/LP, 10 benign/likely benign, and 3 remain VUS. The article demonstrates that in silico prediction tools alone (SpliceAI, MaxEntScan) are insufficient to resolve splicing VUS: functional RNA assays remain necessary for ambiguous cases. New PVS1_RNA and BP7_S(RNA) criteria replace PS3/BS3 for splicing-affecting variants.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

New ClinGen SVI Splicing Subgroup 2026 criteria are directly actionable in ACMG classification pipelines of laboratories processing BRCA1/BRCA2. The demonstration that SpliceAI alone is insufficient for complex splicing VUS is an important practical message. Integrate into institutional classification procedures as soon as possible.

new PVS1_RNA + BP7_S criteria (ClinGen SVI 2026) +2; BRCA1/BRCA2 high clinical impact +2; Clin Chem (top lab med journal) +2; applicable to classification pipelines +1