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NCBI Resources: ClinVar

Contains information about the NCBI databases to be used as a teaching tool.

ClinVar Unique Identifiers

  • Variation ID: 6 digit number for all the variants found in one observation
  • Allele ID: 6 digit number for each individual variation in the DB.

Boolean Operators

Boolean operators allow you to combine search terms: 

  • AND: Finds documents that contain both terms.
  • OR: Finds documents that contain either term. 
  • NOT: Finds documents that contain the term on the left but not the term on the right.

Advanced Search

By default, Entrez searches your text in "All fields", which looks for the text anywhere in the entry. So if you're getting irrelevant results, try limiting your text to a particular field.

Don't know what fields you can search for? Use the Advanced search

1. Click on advanced beneath the search bar. 

2. Click the drop down menu under Builder to see what fields are stored in gene records.

This is a comprehensive list of all fields you can search for. Fields will vary by database. Example shown here is for the Gene database. 

Need help? Ask Wlad

Searching ClinVar

You can search ClinVar by:

ClinVar Results

After submitting your search, a list of results will appear with gene records that match your query. The results page is divided into 3 columns:

  1. Filters: more ways to limit your search by things like genome location
  2. Results: a list of the Gene records that match your query with basic information
  3. Discovery Column: links to other databases and Search details

You can use the filters to limit your results by factors like pathogenic variants, type of mutation (eg, missense) and type of variation (eg SNP).

The center column contains record previews that show you the location of the variation, the genes involved, the Conditions associated with that variation, how common the variation is, the clinical significance of the variation, and how these assertions were made (level of evidence).

To access and individual record, click on the variation link in the first column of the table. 

ClinVar record

ClinVar contains information about

  • Pathogenicity of the variation
  • Association with conditions
  • Alleles
  • Clinical assertions 
  • Summary evidence
  • Supporting observations

See the following link for an example: 

http://www.ncbi.nlm.nih.gov/clinvar/variation/17878/