HGVS

This class of variant refers to any variant that can be coded using transcript-based HGVS nomenclature (from the Human Genome Variation Society (HGVS)). In practice, these are relatively small (usually less than 25 nucleotides) changes that are located within the transcript sequence of a gene.

Phenoboard operates on a cohort-basis in which one transcript of reference is used for the entire cohort. For instance, if we wanted to code this variant: NM_000138.5(FBN1):c.8057G>T (p.Cys2686Phe), then the transcript (NM_000138.5), would be available for the entire cohort and we would enter c.8057G>T (only). Variants in non-coding transcripts, such as NR_003137.3(RNU4-2):n.69C>T can be entered using the "n." notation (in this example we would enter n.69C>T]).