Registry Human Genome Variation Society Nomenclature

The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the HGVS Variant Nomenclature Committee (HVNC) under the auspices of the Human Genome Organization (HUGO).

Prefix: hgvs
Links: Homepage Repository Request Discussion
Publications: 2016 HGVS Recommendations for the Description of Sequence Variants: 2016 Update; 2014 A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature
References: GitHub Issue https://github.com/biopragmatics/bioregistry/issues/460

Identifier Standards

Pattern for Local Unique Identifiers: Missing LUI pattern
Example Local Unique Identifiers: NP_003997.1:p.Trp24Cys Resolve
GRCh38(chr11):g.112088970del Resolve
NC_000011.10(NM_001276503.2):c.169+998del Resolve
NC_000011.10:g.112088970del Resolve
NG_012337.3(NM_003002.4):c.274G>T Resolve
NG_012337.3(NM_003002.4):r.(274g>u) Resolve
Example CURIEs: hgvs:NP_003997.1:p.Trp24Cys
hgvs:GRCh38(chr11):g.112088970del
hgvs:NC_000011.10(NM_001276503.2):c.169+998del
hgvs:NC_000011.10:g.112088970del
hgvs:NG_012337.3(NM_003002.4):c.274G>T
hgvs:NG_012337.3(NM_003002.4):r.(274g>u)

Contacts

Contact: Reece Hart 0000-0003-3463-0775 reece
Contributors: submitter Madeline Iseminger 0000-0002-0548-891X miseminger
Reviewer: Charles Tapley Hoyt 0000-0003-4423-4370 cthoyt

Mappings to External Registries

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 2 mappings to external registries with 2 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix	Curate
HL7	`hl7`	`2.16.840.1.113883.6.282`
Wikidata	`wikidata`	`P3331`

Providers

Suggest

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier NP_003997.1:p.Trp24Cys is used to demonstrate the providers available for Human Genome Variation Society Nomenclature. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Provider Name	Provider Code	URI
Human Genome Variation Society Nomenclature	`hgvs`	http://reg.clinicalgenome.org/allele?hgvs=NP_003997.1:p.Trp24Cys
Bioregistry	`bioregistry`	https://bioregistry.io/hgvs:NP_003997.1:p.Trp24Cys

Extra Providers

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.

Provider Name	Provider Code	URL
LUMC Mutalyzer 3	`mutalyzer`	https://mutalyzer.nl/api/description_to_model/NP_003997.1:p.Trp24Cys

This name annotation was originally annotated in Bioregistry and is redistributed under the CC0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("hgvs")
'Human Genome Variation Society Nomenclature'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("hgvs")
'https://hgvs-nomenclature.org/stable/background/simple/'

Get the repository:

>>> import bioregistry as br
>>> br.get_repository("hgvs")
'https://github.com/HGVSnomenclature/hgvs-nomenclature'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("hgvs")
'Reece Hart'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("hgvs")
'reecehart@gmail.com'

Get the contact's GitHub handle:

>>> import bioregistry as br
>>> br.get_contact_github("hgvs")
'reece'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("hgvs")
'0000-0003-3463-0775'