Identification and correct classification of disease-associated mutations are essential for molecular diagnosis and clinical management of many genetic disorders. Although next-generation sequencing has greatly accelerated the detection of nucleotide changes, the biological interpretation of most variants has become a real challenge. Moreover, attention is typically paid to protein-coding changes and the potential impact of exonic variants on RNA splicing is often ignored. There is increasing evidence showing that disease-causing aberrant RNA splicing is more widespread than currently appreciated. Here, we review the major types of the variants involved in RNA splicing and the approaches used to identify and characterize these variants. We hope to provide a reference for evaluation of the effects of mutations on diseases.