How to understand clinvar database

Today, I will talk to you about how to understand the clinvar database, many people may not know much about it. In order to make you understand better, the editor has summarized the following for you. I hope you can get something according to this article.

Clinvar and OMIM databases are similar in that they store the relationship between human variation sites and phenotypes.

Clinvar is an open database to which each research institution can submit data, and a team of experts will review and rate the submitted information. The sites in the database are divided into 1 to 4 different stars according to the reliability of the annotation information. the higher the star level is, the higher the credibility is. As of May 29, 2018, all records in the database are as follows

It can be found that in the whole database, the variation sites of 3 stars and 4 stars are very few, and the most are 1 star variation sites.

In this database, the following seven retrieval methods are provided

Gene symbols

HGVS expressions

Protein change

Rs number

Disease

Submitters

Location on a chromosome

Taking the gene symbol of PTEN as an example, some of the records retrieved are as follows:

For each record, the following three types of information are given.

1. Basic comment

For the record of each variation site, there is a Variation ID and a corresponding star score.

The meanings of different star level representatives are as follows:

2.Interpretation

This section will give the clinical significance of the mutation site Clinical significance, and links to related databases, which usually contain MedGen, OMIM, dbSNP, PubMed and so on.

3. Allele

This section gives the details of allel, including variation types, HGVS expressions, and so on.

We can download the database directly through the FTP service. The link is as follows

Ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/

A variety of formats are provided on the ftp server, usually you can choose VCF to download, and both hg19 and hg38 versions of vcf files are given at the same time.

After reading the above, do you have any further understanding of how to understand the clinvar database? If you want to know more knowledge or related content, please follow the industry information channel, thank you for your support.