A Plot Twist: When RNA Yields Unexpected Findings in Paired DNA-RNA Germline Genetic Testing

Area of Science:

• Genetics
• Molecular Biology
• Bioinformatics

Background:

• Germline genetic variants affecting RNA splicing are a significant cause of human disease.
• Interpreting these variants is challenging due to the complexity of splicing mechanisms.
• Advances in splicing prediction algorithms improve accuracy but predicting aberrant splicing remains difficult.

Purpose of the Study:

• To illustrate the complexities of interpreting genetic variants with unusual splicing impacts.
• To demonstrate how paired DNA and RNA testing can avoid pitfalls in variant interpretation.
• To expand the understanding of clinically relevant splicing mechanisms.

Main Methods:

• Retrospective review of patient data with concurrent DNA and RNA testing.
• Analysis of seven rare variants exhibiting unusual splicing impacts.
• Case-based exemplars to highlight interpretation challenges and solutions.

Main Results:

• A variant at a consensus donor site showed no splicing impact (NF1 c.888+2T>C).
• A mid-exonic variant caused pseudo-intronization via a novel donor and cryptic acceptor site (BRIP1 c.727A>G).
• Other variants demonstrated spliceosome switching (LZTR1), obviated nonsense-mediated decay (APC, BRCA2), and involved pyrimidine tract optimization (NF1, ATM).

Conclusions:

• Paired DNA and RNA testing identified unexpected splice events that altered variant interpretation.
• These findings expand knowledge of clinically significant splicing mechanisms.
• The study underscores the value of RNA testing in genetic diagnostics.