I would like to ask if there are some known databases that allows to annotate non-coding mutations in a given region for the human genome?
Preferably, if the database is downloadable so I am able to automatize the processes of annotation.
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1$\begingroup$ What do you mean with non-coding mutations? SNPs? Check dbSNP. $\endgroup$– bennCommented Aug 27, 2019 at 9:07
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$\begingroup$ What sort of annotations are you looking to include? Ensembl's VEP is great for annotation, and can include many different annotations applicable to both coding and non coding regions, e.g. minor allele frequency, conservation, pathogenicity predictions through CADD (via a plugin) and many other things $\endgroup$– JenGCommented Aug 27, 2019 at 9:59
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$\begingroup$ @benn yes SNPs, I know about dbSNP, I wanted to know if there are other known databases ! $\endgroup$– user324810Commented Aug 27, 2019 at 12:09
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$\begingroup$ @JenG I have VEP installed on my cluster ! but CADD also comes with dbSNP plugin, but thanks I will have a look on it $\endgroup$– user324810Commented Aug 27, 2019 at 12:10
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1$\begingroup$ We could give you better answers if you explained what sort of information you are looking for. What kind of "annotating" do you need? $\endgroup$– terdon ♦Commented Aug 27, 2019 at 13:29
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1 Answer
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VarSome allows you to annotate any variant, including non coding ones. While ACMG classification will not be available if the variant isn't in a gene's transcript (the ACMG criteria are only applicable to variants in transcribed regions), non-coding variants in transcripts will be fully annotated. For example, if you look up variant chr17-41197559-G-T which is a non-coding variant found in the UTR of one of the transcripts of BRCA1, you will get a lot of information (probably best to click on the link, the image has a lot of data):
For non-coding variants that don't fall in any transcript, you can still get frequency data, when available, as well as DANN pathogenicity predictions, GERP score, an overview of the genomic regions and other variants and/or srtuctural variants that can be found around the region, and any community annotations that may have been submitted by other users.
There is also an API you can use to automate the annotation, and VarSome Pro that lets you annotate an entire VCF file, but those are both paid services.
Disclaimer: I work for the company behind VarSome.
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$\begingroup$ This looks interesting but yikes I don't think it would be much of use in my case since automating the annotation is in my needs. Thanks though. $\endgroup$ Commented Aug 27, 2019 at 12:15
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$\begingroup$ @Law yeah, the API and/or the Pro version where you can send VCFs would probably be helpful for you, but those aren't free. I thought I'd mention them in case you do have a budget. $\endgroup$– terdon ♦Commented Aug 27, 2019 at 12:23