Authorities used in ClinVar

A major function of ClinVar is to harmonize submissions from diverse sources by converting data elements to standard terms and/or public database identifiers.  This page summarizes how different elements are managed, and provides links to current authoritative content.

  1. Nomenclature
  2. Ontologies
  3. HGVS
  4. Clinical significance
  5. More...

Nomenclature

ClinVar uses official terminology when available. The authorities for names of conditions and clinical features, genes, and proteins are detailed on our Nomenclature page.  The nomenclature is shared among ClinVar, Gene, and the NIH Genetic Testing Registry (GTR).

Ontologies

Sequence Ontology

The European Bioinformatics Institute (EBI) and NCBI collaborate on standardizing the representation of types of variation and their molecular consequences according to the Sequence Ontology. The identifiers for the terms are referenced in ClinVar. More...

VariO

ClinVar uses Variation Ontology to represent the effects and consequences of variation.

HGVS

ClinVar represents variation according to the HGVS standard. Submitters may describe alleles in any of the subset of HGVS expressions described here, or as sequence changes relative to top-level genomic sequences defined by the Genome Reference Consortium or NCBI's Reference sequences.  ClinVar then computes alternate expressions, and reports the results in specific types as detailed here.

Clinical significance

The NCBI databases, including ClinVar, will adhere to the standard of the American College of Medical Genetics (ACMG) when the terminology has been revised. The list of terms currently used by ClinVar and GTR are reported on GTR's ftp site: ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Clinical_significance.txt.

NCBI also maintains a page to document how clinical significance is determined and reported.

More...

A comprehensive listing of the terms on which GTR and ClinVar standardize content is provided for ftp transfer ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/. The README file on that site provides more details.

Last updated: 2014-04-22T08:48:09-04:00