Variants

Phenoboard can be used to code and Q/C three kinds of variant.

1. 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]).

Symbolic structural variants

Data about large structural variants is often provided in an imprecise fashion in the literature, e.g., "DEL ex3-5". Phenoboard supports this. Users should provide the category of structural variant (DEL, DUP, INS, INV, TRANSLOCATION) if possible or otherwise indicate simply "SV".

Intergenic variants

Promoter and enhancer variants outside of the transcript of a gene cannot be represented using transcript-based HGVS notation. Instead, the accession number of the chromosome (in HG38) and the corresponding genomic HGVS nomenclature should be provided.

For instance, NC_000019.10:g.12887294G>A is a promoter variant upstream of the KLF1 gene.