Human Genome Variation Society (HGVS) Nomenclature

The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA, and protein sequence variants. In brief, HGVS defines a way of representing variants as compared to a reference sequence. For instance, c.435A>GA represents a substitution at position 435 of the sDNA (Adenine changed to Guanine). See the HGVS website for details.

This page provides advice about how to correct and check possibly incorrect variant nomenclature found in the literature.

Transcript

It is essential to indicate the sequence (usually a transcript) of reference. For mRNAs, the MANE Select sequence should be used if possible. We tend to obtain this sequence from the HGNC page for a gene.

Variant Validator

The VariantValidator API is used by HRMDBQ. While a difficult variant is being investigated, we highly recommend using the website (under Tools/Validator).

Arrows

Variants such as c.-113A → C are now written as c.-113A>C.

Odd characters

Many publications put (nearly) invisible whitespace between the numerical part and the nucleotide symbols. All white space should be removed.