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BioCodeKb - Bioinformatics Knowledgebase

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible. ClinVar supports submissions of differing levels of complexity. The submission may be as simple as a representation of an allele and its interpretation (sometimes termed a variant-level submission), or as detailed as providing multiple types of structured observational (case-level) or experimental evidence about the effect of the variation on phenotype. A major goal is to support computational (re)evaluation, both of genotypes and assertions, and to enable the ongoing evolution and development of knowledge regarding variations and associated phenotypes. ClinVar is an active partner of the ClinGen project, providing data for evaluation and archiving the results of interpretation by recognized expert panels and providers of practice guidelines. ClinVar archives and versions submissions which means that when submitters update their records, the previous version is retained for review.

The level of confidence in the accuracy of variation calls and assertions of clinical significance depends in large part on the supporting evidence, so this information, when available, is collected and visible to users. Because the availability of supporting evidence may vary, particularly in regard to retrospective data aggregated from published literature, the archive accepts submissions from multiple groups, and aggregates related information, to reflect transparently both consensus and conflicting assertions of clinical significance. A review status is also assigned to any assertion, to support communication about the trustworthiness of any assertion. Domain experts are encouraged to apply for recognition as an expert panel.

Accessions, with the format SCV000000000.0, are assigned to each submitted record. If there are multiple submitted records about the same variation/condition pair, they are aggregated within ClinVar's data flow and reported as a reference accession with the format RCV000000000.0. ClinVar archives submitted information, and adds identifiers and other data that may be available about a variant or condition from other public resources. However ClinVar neither curates content nor modifies interpretations independent of an explicit submission.

ClinVar recieves submissions from:

  • clinical testing labs

  • researchers

  • genetics clinics

  • locus-specific databases

  • expert panels

  • groups establishing practice guidelines

Recent improvements to searching in ClinVar include:

  • Variants may be searched based on the date that the clinical significance was last evaluated by a ClinVar submitter. This feature was added to make it easier to focus on records that were interpreted within a particular time period.

  • Variants in specific genes may be searched by HGNC_IDs (11), as well as by GeneIDs (5), e.g. 1100[hgnc].

  • Variants reported with specific phenotypes may be searched by HPO (12) IDs, e.g. ‘hp 0004322’[Trait identifier].


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