ClinVar

How to search ClinVar

• Tutorial
• Common queries
• More complex queries
  • Query strategies
  • Advanced search
• Reviewing the result set
  • Using filters to refine the results
• Understanding the ClinVar web display
• Data standards
• Building URLs

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

Advanced Search

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.

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

• 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.
• Searches for gene symbols and genomic locations also show the results as a graphical display.
• You 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 web display.

Using filters to refine the results

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

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 (the accession starting with VCV), 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 page 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.

Data standards

ClinVar uses established standards for data types such as variation description, variation type, diseases, genes, proteins, and classification. 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. Read about constructing URLs to ClinVar.