Fig. 8

The importance of multiple alternative transcripts for variant interpretation. This hypothetical example of gene ‘AGENE’ expressed in brain highlights how the same variant could have different outcomes in different transcripts. We illustrate this further using hypothetical HGVS nomenclature. Note that when there are multiple transcripts for a gene, this can have an effect on amino acid numbering of variants as different transcripts can have different exon combinations, meaning that the same exon in two different transcripts can have a different translation and can also result in different lengths for the amino acid sequence. Note too that the untranslated region is represented by orange boxes. Green boxes represent the coding sequence (CDS), whereas purple boxes represent the CDS of the nonsense-mediated decay (NMD) transcript. Lines that join exons represent introns. Asterisks indicate the positions of the following hypothetical variants. (1) NM_000000001.99(AGENE):c.2041C > T (p.Arg681Ter). This variant might not be of interest to the clinician as it lies in an exon that is not expressed in brain. (2) NM_000000002.99(AGENE):c.4002 + 2451G > C. The Human Genome Variation Society (HGVS) suggests that this variant is intronic, yet, by looking across other transcripts, it is clear that the variant falls in an extended coding exon that is expressed in brain. (3) NC_000000003.99:g.66178947G > T. This variant is intronic to the canonical transcript, but falls in a well-conserved exon that is expressed in brain. (4) ENSP0000000004.1(AGENE):p.Gly276Ala. This variant falls in an exon that induces NMD. The exon is well conserved and expressed in the brain, making it potentially relevant to the clinician. Generally, NMD transcripts have been considered to be non-coding and excluded from sequence analysis. However, such exons are now known to have an important role in gene regulation. For example, Lynch and colleagues [194] reported that variation in the highly conserved exon in SNRPB that induces NMD can result in severe developmental disorders