How to search ClinVar

Common queries

Go to the search box in the gray area at the top of the page. Just type your search term, and click on the Search button to the right of the search box. ClinVar can be searched with terms like:

More complex queries

ClinVar uses the same type of query interface you may be familiar with if you use PubMed or other databases at NCBI. In other words, when you enter a term or phrase of interest in the query box, that term or phrase will be processed to retrieve records that contain or have some relationship to the word(s) you entered. The information is also organized into information categories or fields, so that queries can be constructed that retrieve records only if the term of interest occurs in that field. If you know the name of the field, you can enter that field name yourself. Otherwise you can use the Advanced page to help you build your query.

Query strategies

Purpose

Examples

(try the link)

Comments
Find records for a particular disease or phenotype "breast cancer"[dis]
  • If you enter the name of the disease or phenotype followed by [dis], your results include variations reported for that disease/phenotype.
  • If you do not include [dis], your results include records where the disease/phenotype is anywhere in the record, not necessarily reported for that variant.
  • *is used as the wild card. It can be used only at the end of a word.
Find records for a particular gene BRCA1[gene] If you enter the gene symbol followed by [gene], your results include variations that affect that gene.

Gene sensor function

Search ClinVar for CFTR.

If your query is a gene symbol that ClinVar recognizes, your search results include variations that affect that gene.

You also get the option to search for that gene symbol anywhere in ClinVar records, e.g. a record for a CFTR variation may have a comment that mentions the TGGB1 gene:

Showing for results for variants in theCFTRgene.Search instead for all ClinVar records that mentionCFTR).

"Did you mean" function

Search ClinVar using CFTR pathogenic.

If your query is more than a single word, and ClinVar detects that one of those words is a gene symbol, then ClinVar asks if you want to process your query as a gene symbol or review data in NCBI's Gene database.

Did you meanCFTRas a gene symbol?Search ClinVar for CFTR

SeeCFTR cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)in the Gene database)

Find records by position on a chromosome for an assembly 17[chr] AND 43000000:44000000[chrpos37] The [chrpos],  [chrpos37], and [chrpos38] fields support queries by range, where the range separator is a colon (':').   Don't forget to provide the value for chromosome as well.

Advanced is very useful when you want to construct a query that combines several concepts and/or restrict values to specific fields.

  1. Click on Advanced in the gray query bar.
  2. Browse for terms that may be anywhere in the database (All Fields) or in a particular field (selected from the menu of field names).
  3. Combine your search term with others using AND , OR or NOT in the menu to the left of the next query term.

We provide more details on using Advanced Search .

Name Abbreviation Scope and explanation
Table 2. Fields in ClinVar
Allele ID [alleleid] The ClinVar identifier for an individual change. e.g. for a haplotype of five SNPs, each individual SNP has its own Allele ID.
Base position

[chrpos]   [cpos]

[cposition]

[chrpos38]

The chromosome base position, based on the current reference assembly (GRCh38).
Base position for assembly GRCh37

[chrpos37]

[C37] [C37POSITION]

The chromosome base position on GRCh37/hg19.
Chromosome

[chr]   [chrm]

[chromosome]

The chromosome(s) on which a variant is found.
ClinVar accession [clv_acc] The SCV or RCV accession number for a ClinVar record. Querying with an RCV retrieves the RCV record as well as its component SCV records. Querying with an SCV retrieves the SCV record as well as its aggregate RCV record.
Complexity [cmplx] Complexity of variant combinations, such as haplotypes and compound heterozygotes.
Creation Date

[cd]

[cdat]

Date the record was created.
Cytogenetic band

[cytgen]

The cytogenetic location for a variant.
Disease/Phenotype [dis] Disease or trait associated with a variant.
External allele ID Identifiers for alleles/variants from sources other than ClinVar, such as OMIM allelic variant ID, IDs from LSDBs, rs#, or dbVar identifiers.
Filter

[sb]

[filter]

These filters represent the infrastructure to link between ClinVar and other Entrez databases.

Filters based on links to other records:
clinvar_all[Filter]  < a href="/clinvar?term=%22clinvar_all%22[Filter]">try in ClinVar
clinvar_dbvar[Filter]try in ClinVar
clinvar_gene[Filter]try in ClinVar
clinvar_medgen[Filter]try in ClinVar
clinvar_omim[Filter]try in ClinVar
clinvar_pmc[Filter]try in ClinVar
clinvar_pubmed[Filter]try in ClinVar(based on citations provided in ClinVar records)
clinvar_pubmed_calculated[Filter]try in ClinVar(calculated based on matching gene and text of a variant description)
clinvar_snp[Filter]try in ClinVar

These filters are more general
all[Filter]ClinVar

Gene Full Name [gene_full_name] Full name for a gene of interest.
Gene ID [geneid] GeneID for a gene of interest.
Gene Name [gene] Symbol for a gene of interest.
HGNC identifier for human gene [hgnc] HGNC identifier for a gene of interest.
Last interpreted [clinsig_last_eval] The date that a variant was last interpreted by a submitter. In other words, the date is for each submission or SCV, not the aggregate record.
Length of the variant [varlen] The length of the variant. For insertions and duplications, this is the length of the inserted or duplicated sequence.
MIM [mim] MIM number from OMIM.
Modification Date

[moddate]

[mdat]

Last date the record was modified.
Molecular consequence [molcons] Calculated result of the indicated allele based on difference relative to reference.
Name of the ClinVar record [titl] The ClinVar record name, which is the combination of the variant name and phenotype name, e.g.

NM_000492.3:c.1521_1523delCTT AND Cystic fibrosis

Organism [orgn] Scientific and common names of organism. Currently all ClinVar records are for human variants and disorders/phenotypes.
Origin [origin] The origin of the variant allele.de novovariants are represented asde novo, not by the maternal/paternal origin of the chromosome with thede novovariant.
Properties [prop] Terms in the property field are standards used to categorize records in ClinVar. Properties include values for clinical significance, mode of inheritance, and others. The full list of properties, and their definitions, areprovided in this document.
PubMed ID [pmid] PubMed IDs linked to the clinical assertion record.
Review status [revstat] Review status of the record.
Study Name [studyname] The name of the study in which the variant was assessed, such as CSER.
Submitter [subgrp] The name of the submitter. Each word of the name is processed independently.
Submitter Batch [subid] The name of a batch of submissions from a submitter. This corresponds to "Submission name" on the submission spreadsheet.
Taxonomy ID

[taxid]

[tid]

Identifier for the species in the NCBI taxonomy database. Currently all ClinVar records are for human variants and disorders/phenotypes.
Text Word [text] Any word in a ClinVar record.
Trait identifier [traitid] Trait identifiers, such as CUI or HPO.
Type of variation [vartype] Type of variation represented in the record.
Variant name [varnam] Name of the allele.
Variation ID [uid] The ClinVar identifier for the variant or set of variants that were interpreted. e.g. for a haplotype of five SNPs, the set of five SNPs has a single Variation ID (or unique identifier - UID).

Reviewing the result set

Currently, you can view a search result set in two formats.

  • The default is a tabular display. You can re-sort the table by gene or genomic location with the "Sort by..." menu at the top.
  • You can change the format from Tabular to "Summary" to view the results as a paragraph-like summary.

When you search ClinVar, you are searching for variants, not for individual submissions. For example, "create date" is the date that the aggregate variant record was first created, not the date that an individual submission, or SCV, was created. Similarly, a search for 'genedx[Submitter] AND "clinsig pathogenic"[Properties]' results in variants for which GeneDx is a submitter and there is an interpretation of "pathogenic", but not necessarily variants that GeneDx classified as "pathogenic".

Using filters to refine the results

You can refine your search results further using the filters to the left of the results.

Filter name How to use the filter
Gene

Set up custom gene filters. This is useful if you often limit your results to certain genes:

  1. Click "Customize this list"
  2. Start typing the gene symbol e.g. BRAF
  3. Click "Show"; this adds a filter for the BRAF gene
  4. Click "BRAF" in the filters to limit your search results to variants that affect BRAF
Clinical significance

Theclinical significance reported by submitters. This may be different from theoverall clinical significance for the variation.

For example, if you limit your results to Pathogenic , the results include all variations with a submitted interpretation of Pathogenic on an SCV. The overall clinical significance for the variation may be Pathogenic, Likely pathogenic/Pathogenic, or conflicting interpretations of pathogenicity.

Review status Thereview status of the variation. You can limit results to variations where at least one submitter provided assertion criteria with the filter "at least one star".
Allele origin The reported origin of the variation.
Method type The collection method. This filter lets you limit your results to variations with reports from clinical testing, research, or literature reports ("literature only").
Molecular consequence The molecular consequence of the variation, calculated by NCBI.
Variation type The type of variation.
Complexity

This filter lets you limit your results to variants reported as single variants or as combinations:

  • Simple - a single variant
  • Haplotype - two or more variants on the same chromosome interpreted together
  • Compound heterozygote - two variants as a compound heterozygote interpreted together
  • Phase unknown - two variants interpreted together but phase is unknown
  • Distinct chromosomes - two or more variants in different genes on different chromosomes interpreted together
Variant length The length of the variant sequence. This filter is useful to distinguish between smaller sequence variants and larger structural variants.
If you select multiple options within a filter, the results will include records with any of the selected options within that filter. Note that as you make multiple selections within a category, the numbers displayed next to each filter value will change to reflect what is now present in your result set.

If you make selections for more than one filter, the results will include records that match the combination of filters selected.

For example:

  • if you select
    • Pathogenic under Clinical significance
    • Clinical testing under Method type
    • Copy number gain under Variation type

the query results include variations that are copy number gain and were reported pathogenic and are from clinical testing.

  • if you select
    • Probably pathogenic under Clinical signficance
    • and Pathogenic under Clinical significance

the query results include variations that were reported as either Probably pathogenic or Pathogenic.

In Boolean terms:

  • within a filter category, multiple selections are processed as the boolean OR
  • between categories, they are processed as the boolean AND

The first query above is processed as ("clinsig pathogenic"[Properties] AND "study clinical testing"[Properties] AND "copy number gain"[Type of variation])

The second query above is processed as  ("clinsig likely pathogenic"[Properties] OR "clinsig pathogenic"[Properties])

You can also use the Advanced search function to construct complex queries like these.

Understanding the ClinVar web display

The primary web display in ClinVar is a variation-centric page that aggregates information submitted for a variation for all of the reported conditions, along with details for each submission about the variation (the accession starting with SCV). Read more detailed information on the ClinVar variation display .

In addition, there is a ClinVar record report that is specific to the combination of variation and disease, represented by the summary accession in ClinVar (the accession starting with RCV). This page also includes details for each submission about the variation and disease (the accession starting with SCV). Read more detailed information about the ClinVar record display .

Compare the two types of web display .

Data standards

ClinVar uses established standards for data types such as variation description, variation type, diseases, genes, proteins, and clinical significance. You can find more information in our documentation for HGVS usage , nomenclature , and authorities .

Building URLs

You can construct URLs to query ClinVar, or to display a specific record if you know the accession number. See our detailed information about constructing URLs to ClinVar .

Support Center

Last updated: 2018-05-31T14:02:43Z