ClinVar Help

 

Table of Contents

  1. Quick start
  2. How to find information
  3. Reviewing the result set
    1. Using filters to refine the results
  4. Understanding the accession-based display
  5. Data standards
  6. Building URLs

ClinVar Quick Start

Questions can be entered by entering any term, by selecting from a list of selected terms, or by using filters and the Advanced search function to ask more complex questions.

Query strategies

Purpose

Examples

(try the link)

Comments
 
Find records for a particular disease "breast cancer"[dis] If you enter the name of the disease or trait followed by [dis], clinical assertions for variants with respect to that disease will be retrieved. If you do not include [dis], your query is processed by looking for a match on a word or phrase. * is used as the wild card, and that wild card 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], the diseases caused by or with some association to variations within that gene will be retrieved.

Gene sensor function

Search ClinVar for CFTR.

If your query is a single word, and ClinVar detects that the word is a gene symbol, then ClinVar processes the query as a gene symbol, tells you that it did so, and allows you to override the default in case that was not your intent (e.g. Showing for results for variants in the CFTR gene. Search instead for all ClinVar records that mention CFTR).

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 mean CFTR as a gene symbol? Search ClinVar for CFTR

See CFTR 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] and [chrpos37] fields support queries by range, where the range separator is a colon (':').   Don't forget to provide the value for chromosome as well.

 

How to find information

  1. Simple queries
  2. Using Advanced search and the Advanced Search Builder
    1. Using fields
    2. Using properties

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.

Simple queries

Just type your search term, and press enter or click on the Search button to the right of the query box.

Using advanced search and the Advanced Search Builder

Click on Advanced in the query bar to access this tool. Advanced is very useful when you want to construct a query that combines several concepts and/or restrict values to specific fields. The interface allows you to browse for terms that may be anywhere in the database (All Fields) or in a particular field (selected from the menu of field names). Each search term can be combined with the others by the choice of AND, OR or NOT provided to the left of the next query term. Documentation of the mechanics of using Advanced Search Builder is provided here.

Name Abbreviation Scope and explanation
Table 2. Fields in ClinVar
Base position

[chrpos]   [cpos]

[cposition]

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 will retrieve the RCV record as well as its component SCV records. Querying with an SCV will retrieve 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.
Disease/Phenotype [dis] Disease or trait associated with a variant.
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.
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   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 phenotypes.
Properties [prop] Terms in the property field are standards used to categorize records in ClinVar. 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.
Submitter [subgrp] The name of the submitter. Each word of the name is processed independently.
Taxonomy ID

[taxid]

[tid]

Identifier for the species in the NCBI taxonomy database. Currently all ClinVar records are for human variants and 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 ID [varid] Variant identifiers, such as OMIM allelic variant ID, IDs from LSDBs, rs#, or dbVar identifiers.
Variant name [varnam] Name of the allele.

Reviewing the result set

Currently, a search result set can be reported in two formats. The default is a tabular display that can be re-sorted by gene or genomic location based on the options listed in the Display Settings menu at the top. The Display Setting options can also be used to provide the results as a 'standard' paragraph-like summary.

Using filters to refine the results

Search results may be refined further using the filters to the left of the results. Result sets may be filtered by clinical significance, review status, method of data collection, molecular consequence, and variation type. Note that within a filter cateogory, multiple selections are processed as the boolean OR to allow you to select more than one option within that category . Between categories, they are processed as the boolean AND.

In other words, if you select the filters Pathogenic under Clinical significance, Clinical testing under Method type, and Copy number gain under Variation type, the query would be processed as if you entered ("clinsig pathogenic"[Properties] AND "study clinical testing"[Properties] AND "copy number gain"[Type of variation]).  But if you select Proably pathogenic and then Pathogenic, the selection is processed as  ("clinsig likely pathogenic"[Properties] OR "clinsig pathogenic"[Properties]).  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.

Please note you may always use the Advanced function to construct complex queries.

Understanding the ClinVar web display

The primary web display in ClinVar is a variation-centric report, that aggregates information submitted for a variant independent of the associated conditions. More detailed information on the ClinVar variation display is available. In addition, there is a ClinVar record report that displays the content of each summary accession in ClinVar (the accession starting with RCV), along with details for each individual accession (the accession starting with SCV). More detailed information about the ClinVar record display is also available. A comparison of the two types of web display is also provided.

Data standards

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

Building URLs

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

Last updated: 2015-05-06T21:15:24-04:00