Functional evidence (I) transcripts and RNA-splicing outline

Abstract A significant proportion of the clinically relevant genetic variants affect the splicing process (spliceogenic variants), but not all spliceogenic variants are necessarily pathogenic. In this chapter, we will review different methodologies and best practices to assess the spliceogenic effect of a suspected variant and, equally relevant, to perform an accurate clinical interpretation of the spliceogenic findings. This chapter will deal as well with a related but different topic. Virtually all human genes undergo alternative splicing, and this fact affects genetic testing at several critical steps, including: (i) selection of target sequences to be tested, (ii) unambiguous designation of genetic variants identified, and (iii) functional interpretation of the findings. The relevance of alternative splicing in genetic testing (traditionally neglected) has been widely recognized by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology in recent standards, guidelines, and recommendations for the clinical interpretation of sequence variants, as will be discussed.