HGVS Recommendations for the Description of Sequence Variants: 2016 Update

By Johan T. den Dunnen, R. Dalgleish, Donna R. Maglott, Reece K. Hart, M. Greenblatt, J. McGowan-Jordan, A. Roux, T. Smith, Stylianos E. Antonarakis, Peter E. M. Taschner. Human Mutation, 2016

1,645 citations recorded by the source corpus.

The consistent and unambiguous description of sequence variants is essential to report and exchange information on the analysis of a genome. In particular, DNA diagnostics critically depends on accurate and standardized description and sharing of the variants detected. The sequence variant nomenclature system proposed in 2000 by the Human Genome Variation Society has been widely adopted and has developed into an internationally accepted standard. The recommendations are currently commissioned through a Sequence Variant Description Working Group (SVD‐WG) operating under the auspices of three international organizations: the Human Genome Variation Society (HGVS), the Human Variome Project (HVP), and the Human Genome Organization (HUGO). Requests for modifications and extensions go through the SVD‐WG following a standard procedure including a community consultation step. Version numbers are assigned to the nomenclature system to allow users to specify the version used in their variant descriptions. Here, we present the current recommendations, HGVS version 15.11, and briefly summarize the changes that were made since the 2000 publication. Most focus has been on removing inconsistencies and tightening definitions allowing automatic data processing. An extensive version of the recommendations is available online, at http://www.HGVS.org/varnomen.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7b04e07f261a30da8656aabef67e07dd58fabba7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

The UCSC Genome Browser database: 2019 update (2018, background): “Since last year, the same search box also accepts Human Genome Variation Society (HGVS) variant nomenclature (23).”
The UCSC Genome Browser database: 2025 update (2024, neutral): “A RefSeq Historical track has been added for the hg38 assembly, enabling the search of previous RefSeq transcript versions, including NM_ accessions and HGVS searches ( 10 ,11 ).”
VarSome: the human genomic variant search engine (2018, background): “Users can search by gene name, transcript symbol, genomic location, variant ID or HGVS nomenclature (2).”
Settling the score: variant prioritization and Mendelian disease (2017, methodology): “…disorders, and both organizations agreed on the need to standardize the description of variants using: Human Genome Variation Society (HGVS) nomenclature 86 , Human Genome Organisation (HUGO) gene identifiers 87 , named reference sequences with versioning, and five grades of clinical significance.”
FlyBase: a guided tour of highlighted features (2022, methodology): “Designations using standardized HGVS nomenclature (den Dunnen et al. 2016) and links to ClinVar (Landrum et al. 2018) are included to facilitate comparison of comparable alleles and to provide descriptions compatible with those used by the medical community.”
COSMIC: a curated database of somatic variants and clinical data for cancer (2023, positive): “Genes, variants, and transcripts use external vocabularies and ontologies—HGNC ( 10 ), Sequence Ontology ( 11 ) and HGVS ( 12 ), or Ensembl ( 13 ), respectively .”