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How to search ClinVar

Common queries

Here are some common ways that ClinVar can be searched:

Search for a specific variant

  • HGVS expressions, e.g. NM_000314.8:c.395G>T
    • This works best on the current version of the RefSeq.
  • Gene symbol and c. or p., e.g. PTEN c.34A>C
    • You may get multiple results, if the gene has multiple transcripts with a variant with that c. description, e.g. MUTYH c.1142G>A
  • "gnomAD format", e.g. 13-32932018-G-A or 13:32932018:G:A for an SNV
  • 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.

  • Variants that result in the same protein change, e.g. BRCA1 S803R
  • rs numbers which represent a type of variation at a location, e.g. rs180177042
  • Variants at the same nucleotide location, e.g. MSH2 c.942
  • Variants in the same codon, e.g. FBN1 p.cys1138 or FBN1 C1138
  • Variants that change an amino acid anywhere in the protein, e.g. FBN1 p.cys

Search for variants within a gene

  • Gene symbol, e.g. PTEN
    • your results may include large structural variants that span the gene. Use the Variant length filter for <1 kb, single gene to limit the results to variants within the gene.

Search for variants within a genomic region

Other types of searches

Search filters

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
Classification type The type of classification available for the variant. Options are germline and somatic; somatic includes both classifications of somatic clinical impact and oncogenicity.
Germline classification The germline classification (formerly called clinical significance) of the VCV record. Note that this may differ from a classification reported by a submitter in an SCV record.
  • If you filter on “Pathogenic”, the results include all VCV records with an aggregate classification 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 classification 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 classification of “Uncertain significance” or “Uncertain risk allele”.
  • If you filter on “Likely benign”, the results include all VCV records with an aggregate classification of “Benign/Likely benign” or “Likely benign”.
  • If you filter on “Benign”, the results include all VCV records with an aggregate classification of “Benign” or “Benign/Likely benign”.
Types of conflicts The type of conflicting classifications for a VCV record. Based on the classification 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 germline classifications 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 size The size of the variant sequence, whether less than or greater than/equal to 50 nt. This filter is useful to distinguish between smaller sequence variants and larger structural variants.
Variant length The length of the variant sequence and whether the variant affects a single gene or multiple genes. This filter is useful to distinguish between smaller sequence variants and larger structural variants, and to exclude multi-gene structural variants from a search with a gene symbol.
Review status The review status of the germline classification for the variant. You can limit results to variants 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 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 Classification
    • 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 Classification
    • Pathogenic under Classification

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.

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 nucleotide 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 GRCh38, the current reference assembly.
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 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 which includes its component SCV records.

Querying with an RCV retrieves the RCV record which includes its component SCV records.

Querying with an SCV retrieves the VCV record that includes the SCV record.
Common name [commonname] A common name for a variant that does not follow a standard like HGVS. For example, deltaF508 or APOE4.
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 phenotype (clinical feature) for which a variant is classified.

This is not an exact search; e.g. searching for autism will return variants classified for Autism, Autism spectrum disorder, Autism spectrum disorder - epilepsy - arthrogryposis syndrome, etc.
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]

The "all" filter returns all records in ClinVar and can be used in combination with other filters to exclude records, e.g. to exclude variants on chromosomes X and Y:
all[Filter] NOT x[Chromosome] NOT y[Chromosome]
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] The consequence of the variant on the transcript, as predicted by the sequence change, e.g. missense, frameshift, intron variant. Molecular consequence is calculated by NCBI, not submitted.
Name of the ClinVar record [titl] The ClinVar record name

e.g for an SNV

NM_000314.8(PTEN):c.1034T>C (p.Leu345Pro)

e.g for a CNV

GRCh37/hg19 10p15.3-q26.3(chr10:100027-135427143)x3
Organism [orgn] Scientific and common names of organism. All ClinVar records are for human variants and conditions.
Origin [origin] The origin of the variant allele, e.g. germline, somatic, de novo, maternal, paternal. De novo variants are represented as de novo, not by the maternal/paternal origin of the chromosome with the de novo variant.
Properties [prop] Terms in the property field are standards used to categorize records in ClinVar. Properties include values for classification (options starting with "clinsig"), mode of inheritance, relationships to genes, and allele origin. The full list of properties, and their definitions, are provided in this document.
PubMed ID [pmid] PubMed IDs linked to the record.
Review status [revstat] Review status of the record.
Study Name [studyname] The name of the study in which the variant was classified, such as CSER.
Submitter Batch [subid] The name of a batch of submissions from a submitter. This corresponds to the "Submission name" registered by the submitter in the ClinVar Submission Portal.
Taxonomy ID

[taxid]

[tid]

 Identifier for the species in the NCBI Taxonomy database. All ClinVar records are for human variants and disorders/phenotypes.
Text Word [text] Any word in a ClinVar record.
Trait identifier [traitid]

Disease or phenotype 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 accession [varacc] VCV accession number for the variant.
Variant name [varnam] A name for the variant, including HGVS expressions, protein changes like V600E, legacy names like Factor V Cambridge.
Variation ID [uid] The ClinVar Variation ID, which is the identifier for the variant or set of variants that were classified. 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 results

  • Search results are displayed as a table. You can re-sort the table by gene or genomic location with the "Sort by..." menu at the top.
  • A search using a gene symbol also shows the results as a lollipop graphic.
    • The gene is shown in its orientation 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 to zoom in on that exon.
    • 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 at the dot, a link to zoom to variants in that region is provided.
  • A search using a genomic region also show the results as a genome view.
    • The results include variants within the region and overlapping the region.
    • 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 their orientation on the chromosome.
    • Each variant that is > 1kb is displayed as a blue bar (copy number gain) or red bar (copy number loss).
    • Each variant that is < 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.
  • You can download the search results as a file using the Download option at the top right. The download includes several more columns of data than the search results on the website.

Last updated: 2025-01-15T20:55:52Z