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Data element name

Sub data element name

Value

Code System Owner

NamePharmacogene Variation Consortium
Websitehttps://www.pharmvar.org/
Email addresssubmissions@PharmVar.org
Phone number
Address
Code System Maintainer (Steward)Name
Website
Email address
Phone number
Address
Code System PublisherName
Website
Email address
Phone number
Address
Code System NamesFormal name of the code systemPharmacogene Variation
Short name of the code systemPharmVar
Code System Technical IdentifiersHTA-endorsed URIhttp://www.pharmvar.org
HTA-endorsed OID
Other URIs
Other OIDs
Case Sensitive Codes (TRUE/FALSE)TRUE (default value)
Code System InformationLinkhttps://www.pharmvar.org/criteria
Notes"The major focus of the Pharmacogene Consortium (PharmVar) is to serve as a repository for allelic variation, providing an official and unified allele designation system for the Pharmacogenetics (PGx) community and facilitating the translation of genotype into phenotype and clinical implementation of PGx. While the majority of pharmacogenes in PharmVar utilize the star nomenclature to describe variation, the provision of single nucleotide variants (SNVs), rather than haplotype, is preferred for some genes.

Thus, PharmVar has two different page formats, A) using star nomenclature and B) using rs ID# as allele (referred to as ‘rs-format’).

PharmVar designates human pharmacogene variation and houses allelic variants in the PharmVar database.

  • All submissions to PharmVar must use the submission form available on www.PharmVar.org and be submitted to submissions@PharmVar.org. Only complete submission requests will be accepted and processed.

  • PharmVar Gene Expert Panels will review each submission and make a recommendation to the PharmVar Steering Committee.

  • In this ‘Allele Designation Criteria and Evidence level’ document, we collectively refer to deviations from the RefSeq as “sequence variations” or “SNVs”, including single nucleotide polymorphisms (SNPs) and small nucleotide insertions and deletions (indels) up to 50 bp. Copy number variants (i.e. entire or partial gene deletions and duplications), hybrid genes (e.g. CYP2D6/2D7 hybrids) and duplications containing non-identical gene copies (e.g. CYP2D6*36+*10) are referred to as CNVs or structural variants.

  • PharmVar applies the following criteria for allele designation. In rare cases, exceptions may be made to accommodate established star allele definitions to minimize impact on research, clinical labs and/or PGx implementation."

In the context of the representation of PharmVar in HL7 standards: 

  • The concept identifier is the PharmVar ID
  • The concept display name is the Allele Name
  • There are several concept properties associated with PharmVar concepts (Legacy Label, Variants, etc.)
  • The code system is represented with an is-a hierarchy
Arrangement or agreements with HL7 for use of content
None
Version management
PharmVar is released monthly (or more frequently) and uses a numbered database version format for each release.
Code System Copyright, Intellectual Property and LicensingCopyright Statement
Copyright Information
Intellectual Property Information
Licensing Information
HTA endorsement status (Draft, In review, Endorsed for use, Pending re-endorsement, Retired) ValueDraft
Assignment date20220920
HTA review statusLast review date
Next review date
Information current as at (date)
20221110

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