Guidelines for clinical interpretation of variant pathogenicity using RNA phenotypes.

Area of Science:

• Genomics
• Molecular Diagnostics
• Bioinformatics

Background:

• RNA sequencing (RNA-seq) is a powerful tool complementing DNA sequencing in molecular diagnostics.
• Aberrant RNA expression, splicing, and allelic imbalance provide crucial information on pathogenic variants.
• RNA-seq has demonstrated a 15% increase in diagnostic rates compared to whole-exome sequencing.

Purpose of the Study:

• To evaluate the utility of RNA phenotypes' statistical significance and effect size as evidence for variant pathogenicity.
• To develop recommendations for integrating functional RNA-seq data into clinical variant classification guidelines.
• To address the lack of formal consensus on assessing variant pathogenicity based on RNA phenotypes.

Main Methods:

• Analysis of 394 pathogenic variants and 723 benign variants.
• Evaluation of RNA phenotypes (expression, splicing, allelic imbalance) as functional readouts.
• Assessment of statistical significance and effect size for variant pathogenicity strength.

Main Results:

• 198 pathogenic variants were associated with aberrant RNA phenotypes.
• RNA-seq provides a high-throughput, transcriptome-wide functional assessment of variants.
• The study quantifies the value of RNA phenotypes in determining variant pathogenicity.

Conclusions:

• RNA-seq data can significantly strengthen variant pathogenicity assessments.
• Recommendations are proposed for incorporating RNA phenotype evidence into established guidelines.
• This work aims to standardize the use of RNA-seq in clinical variant interpretation.