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Fig. 1 | Genome Medicine

Fig. 1

From: A variant by any name: quantifying annotation discordance across tools and clinical databases

Fig. 1

Factors affecting HGVS syntax generation. a Transcript alignment approach can impact the transcript exon structure. Alignment of cDNA sequence by Splign and BLAT to the genome results in a 10-kb difference in an exon positioning in the CARD9 gene (green arrow). b Transcript accession can impact the variant association and HGVS syntax. Here, the identified GNAS variant is outside the clinically relevant transcript. Small changes in versions may also impact the coding sequence. c In the context of nucleotide repeats, variant justification can affect the variant’s position. d Transcript annotation directly impacts its translation to a protein expression. Incorrect transcript annotation can lead to incorrect protein syntax. e Representing the variant in a particular expression. There are different ways of expressing the same coding or protein variant

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