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.## 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:

  • gene symbols, e.g. PTEN
  • gene symbol and c. or p., e.g., mutyh c.1187g>a
  • location / chromosome coordinates, e.g., chr1:11,102,837-11,267,747, 2:144,213,941 - 144,690,824, etc.
  • HGVS expressions, e.g. NM_000314.4:c.395G>T
  • protein changes, e.g. G132V
  • rs numbers, e.g. rs180177042
  • diseases, e.g. cystic fibrosis
  • submitters, e.g. Invitae
  • a ClinVar accession number (VCV, RCV, or SCV). -- searching for a VCV or an RCV accession results in the current version of that record. You can search for a previous version of the record searching by the accession.version. Searching for an SCV accession number, with or without the version, returns the VCV record that includes that SCV.

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 gene BRCA1[gene]
  • If you enter the gene symbol, your results include variations that affect that gene.
  • A lollipop diagram also shows where variants are within the gene.
  • Genes are shown in the orientation they are on the chromosome.
  • A useful strategy to focus a search is to hover over an exon in the Gene track and follow the Exon link in the tooltip.
  • After zooming in, click "Update search results to this region" to synchronize the search results with the lollipop diagram.
  • Hovering over a dot on the lollipop diagram reveals a tooltip with information about the variant. If there is a cluster of variants, a link to zoom to variants in that region is provided.
Find records by chromosome location

chr2:136937000-146682000

GRCh38:2:136937000-146682000

17[chr] AND 43000000:44000000[chrpos37]

  • If you enter a chromosome location, your results include variations within and overlapping that region.
  • A genome view also shows a graphical representation of the variants.
  • When the assembly isn’t specified, like chr2:136937000-146682000, the results are for GRCh37 by default. When the assembly is included, like GRCh38:2:136937000-146682000, the results are on the specified assembly.
  • Genes are shown in the orientation they are on the genome.
  • Each variation > 1kb is displayed as a blue bar (copy number gain) or red bar (copy number loss).
  • Each variation < 1kb is displayed in the Small variant track at the top of the display.
  • Zooming in goes no closer than 1 kb. After zooming in, click "Update search results to this region" to synchronize the search results with the genome view.
  • Hovering over a blue bar, a red bar, or elements on the Small variant map reveals a tooltip with information about the variant.
  • 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.
Find records for a 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.

Advanced search is useful when you want to construct a query that combines several concepts and/or restricts 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 .

ClinVar's Field Name Abbreviation Scope and explanation
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.
Canonical SPDI

[cspdi] [CSPDI]

[Canonical SPDI]

The canonical SPDI notation for the variant. See PMID:31738401 for more information about SPDI.

Example: "NC_000010.11:87925549:T:C"[cspdi]

Chromosome

[chr]   [chrm]

[chromosome]

The chromosome(s) on which a variant is found.
ClinVar accession [clv_acc] The SCV, RCV, or VCV accession number for a ClinVar record.

Querying with a VCV retrieves the VCV record as well as its component SCV records.

Querying with an RCV retrieves the RCV record as well as its component SCV records.

Querying with an SCV retrieves the VCV record that includes the SCV record.
Complexity [cmplx] Complexity of variant combinations, such as haplotypes and compound heterozygotes.
Creation Date

[cd]

[cdat]

Date the VCV 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]
clinvar_dbvar[Filter]
clinvar_gene[Filter]
clinvar_medgen[Filter]
clinvar_omim[Filter]
clinvar_pmc[Filter]
clinvar_pubmed[Filter] (based on citations provided in ClinVar records)
clinvar_pubmed_calculated[Filter] (calculated based on matching gene and text of a variant description)
clinvar_snp[Filter]


This filter finds all records and can be used in combination with other filters to exclude records:
all[Filter]

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 VCV 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, are provided 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 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.

Examples:

HP:0000006 "HP 0000077"[Trait identifier]

ORPHA100 ORPHA100[Trait identifier]

OMIM 219700 219700[Trait identifier]

CUI C0004135 C0004135[Trait identifier]

MeSH D00052 D000052[Trait identifier]

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).

When you search ClinVar, you are searching for variants, specifically the aggregate variant record (VCV), not for individual submissions (SCVs). For example:

  • “Creation date” is the date that the VCV record was first created, not the date that an individual submission (SCV) was created.
  • a search for 'genedx[Submitter] AND "clinsig pathogenic"[Properties]' results in VCV records classified as "pathogenic" that include an SCV from GeneDx but not necessarily an SCV that GeneDx classified as "pathogenic".
  • The only exception is when an RCV record is used as the query; the RCV record is returned.

Reviewing the result set

You can view a search result set in three 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.
  • Change the format from “Tabular” to "Summary" to view the results as a paragraph-like summary.
  • Download the results as a file using the Download option at the top right.

Using filters to refine the results

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

ClinVar's Filter Name How to use the filter
Clinical significance The clinical significance of the VCV record. Note that this may differ from the clinical significance reported by a submitter (SCV).
  • If you filter on “Pathogenic”, the results include all VCV records with an aggregate clinical significance of “Pathogenic”, “Pathogenic/Likely pathogenic”, “Pathogenic, low penetrance”, or “Established risk allele”.
  • If you filter on “Likely pathogenic”, the results include all VCV records with an aggregate clinical significance of “Pathogenic/Likely Pathogenic, “Likely pathogenic”, “Likely pathogenic, low penetrance”, or “Likely risk allele”.
  • If you filter on “Uncertain significance”, the results include all VCV records with an aggregate clinical significance of “Uncertain significance” or “Uncertain risk allele”.
  • If you filter on “Likely benign”, the results include all VCV records with an aggregate clinical significance of “Benign/Likely benign” or “Likely benign”.
  • If you filter on “Benign”, the results include all VCV records with an aggregate clinical significance of “Benign” or “Benign/Likely benign”.
Types of conflicts The type of conflicting interpretations in clinical significance for a VCV record. Based on the clinical significance terms defined above, conflicts are reported between:
  • Pathogenic and/or Likely Pathogenic vs Likely Benign and/or Benign (P/LP vs LB/B)
  • Pathogenic and/or Likely Pathogenic vs Uncertain significance (P/LP vs VUS)
  • Uncertain significance vs Likely benign and/or benign (VUS vs LB/B)
If there are no conflicting interpretations for the variation, this filter is not provided.
Molecular consequence The molecular consequence of the variation, calculated by NCBI.
Variation type The type of variation.
Variant length The length of the variant sequence. This filter is useful to distinguish between smaller sequence variants and larger structural variants.
Review status The review 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".

If you select multiple options within a filter, the results will include records with any of the selected options within that filter. 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
    • Copy number gain under Variation type

the query results include VCV records that are copy number gain and were reported as pathogenic.

  • if you select
    • Likely pathogenic under Clinical signficance
    • Pathogenic under Clinical significance

the query results include VCV records that were reported as either Pathogenic or Likely 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 "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 .

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Last updated: 2022-06-29T13:07:09Z