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The ClinVar variation report

The ClinVar variation page

The ClinVar variation page, or VCV page, displays information from submitters aggregated by each variant (e.g. VCV123456789.1), rather than by the combination of variation-condition that is represented by the reference ClinVar accession (e.g. RCV123456789.1).  The variation page makes it easier to review all the data submitted for a variant, regardless of how the condition was submitted.

ClinVar defines a variation as the set of sequence changes about which a classification has been submitted. Most often a "variation" represents a single variant; more rarely, it represents a haplotype or a genotype.

Title

The title represents the preferred name of the variation.

Read more about how ClinVar calculates a preferred name for each variant.

Classification smmary

The top section shows a summary of the aggregate classifications for a variation based on data from submitters.  The details of what each submitter provided are listed in the Submissions sections.

Read more about how ClinVar calculates aggregate classifications.

Review status (stars)

ClinVar calculates a review status to indicate the level of review supporting each submitted and aggregate classification. Stars provide a graphical representation of the review status on web pages. Read more about the ClinVar review status.

Variant details

The Variant details section summarizes information about the variant, or set of variants, for the classification.

This section includes the Variation ID and the VCV accession and version number. Read more about identifiers in ClinVar.

The data in the Variant details section may come from submitters, but may also be added by NCBI, especially when the variant can be mapped to the genome.  Data usually provided by NCBI include:

  • the type and length of the variant
  • cytogenetic and genomic locations
  • dates for when the variant was first in ClinVar, last submitted, and last evaluated by a submitter for each of the classification types (germline, somatic clinical impact, oncogenicity)
  • HGVS expressions:
    • on the current and previous chromosome sequence (NC accession)
    • on current NM/NPs and RefSeqGene (NG)
    • these may also be provided by submitters
  • molecular consequence: a calculation of the effect of the sequence change, reported per transcript. ClinVar calculates the predicted molecular consequence, but does not predict functional consequence. Functional consequence (e.g. quantitative effects on gene expression, alternative splicing, fuctional impact on the protein) is based on experimental evidence and must be submitted.
  • the protein change, if applicable, e.g. V600E
  • other names for the variant, e.g. deltaF508
  • the canonical SPDI representation
  • GMAF, the global minor allele frequency calculated by the 1000 Genomes Project
  • allele frequency, with the source of the frequency data and the frequency of the stated allele
  • links to related databases, such as dbSNP, dbVar, and Variation Viewer

Genes

The Genes section provides a summary of information about each gene for the variant. Most variants in ClinVar are short and are within a single gene so the Genes section typically shows data for a single gene. CNVs may affect more than one gene; in this case, the Genes table displays the first ten genes, with preference given to genes that have ClinGen Dosage Sensitivity curations. If the CNV affects more than ten genes, there are links to NCBI's Variation Viewer and ClinGen's Dosage Sensitivity curation results to view all the genes in the CNV.

The links for Related variants show you other variants for this gene in ClinVar. The link for "Within gene" shows you variants that affect only this gene, mostly short variants. The link for "All" shows you any variant that affects this gene, including both short variants and CNVs.

Conditions

The Conditions section provides germline- and somatic-specific summaries of conditions that the variant was classified for, including a link to the reference ClinVar record (RCV accession).

Submissions

The Submissions sections display the data from each submitted record (SCV) for the variant. SCVs with a germline classification are in the Submissions-Germline table; SCVs with a somatic classfication of clinical impact or oncogenicity are in the Submissions - Somatic table. In each table, summary-level information is displayed by default; you can expand each row or the whole table to see additional fields, if they were submitted.

Functional evidence

The Functional evidence section displays data from submissions (SCVs) that provide functional consequence. This section is under development. Currently there is no validation to ensure that a description of the method, the result for the assay, and a citation describing the assay are provided in submissions so data may be missing.

Citations

The Citations sections list publications about the variant, most of which are provided by submitters; a small number of citations were curated by NCBI staff.

Citations from SCVs for a germline classification are in the Citations - Germline section; citations from SCVs for a somatic classification of clinical impact or oncogenicity are in the Citations - Somatic table.

These tables include citations about the classification or evidence; it does not include citations about the condition or citations submitted as assertion criteria.

Dates

The date, "Record last updated", shown at the bottom of a VCV record represents the last date that the VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs) or to an update made by ClinVar, e.g. the addition of an HGVS expression or dbSNP rs number.

Other dates reported on the page include:

  • The date "First in ClinVar" in the Variant Details section represents the date when the VCV record first became public in ClinVar for each type of classification.
  • The date "Last evaluated" in the Variant Details section represents the date the variant was most recently evaluated by a submitter for each type of classification.
  • The date "Most recent" in the Variant Details section represents the date of the most recent submission (SCV) for for each type of classification.
  • The date "Last evaluated" in the Submissions section represents the date the submitter last evaluated the variant.
  • The date "First in ClinVar" in the Submissions section represents the date the submitted record (SCV) first became public in ClinVar.
  • The date "Last updated" in the Submissions section represents the date that the latest update to the submitted record (SCV) became public in ClinVar.

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Last updated: 2024-01-29T18:59:07Z