Clinvar vs Snpedia vs DbSNP

Question

[iCode]

I am new to genomics world and just a software guy. I am trying to utilize the better variants databases and confused as what is what. There are several of them.

1. What are the top variants databases that one should use?
2. What is the difference between Clinvar , Snpedia and DbSNP? Should one use all?
3. Are some of these sources focused on a single SNP? what about when few short sequence is different from reference? Clinvar seem to both?

Apologies if my questions are basic.

Answer 1

[tianleivv]

Try ANNOVAR, which combine many databases. And its website has the descriptions of the databases: http://annovar.openbioinformatics.org/en/latest/user-guide/filter/

Answer 2

[finswimmer]

What are the top variants databases that one should use?

You first have to decide what kind of information you need and than choose the database for this purpose, e.g. population frequency data, clinical impact, literature?

If you are interested in population frequency gnomAD is the state-of-the art. But there are other project like 1000Genomes, ExAC, ESP, ...

ClinVar is a good place for getting informations about the clinical impact of a variant.

dbSNP is a database where everyone can submit variants. So the data there doesn't give you much information about the impact of the variant. But the identifier used in dbSNP (rs...) are widely used in other databases to identify the same variant. And it is always a good information that there is someone out there, who find the same variant as you ;)

fin swimmer