chromosomal locations of snps in humvar variant set

Question

[arronslacey]

Hi - in the humsavar dataset there are variants given by protein position and amino acid change. http://www.uniprot.org/docs/humsavar

Is there a way to convert these to chromosome positions and nucleotide changes? thanks.

I should probably add for clarification that some snps listed to do not have an rsid. this is a particularly challenging case because i am not able to join to UCSC snp tracks via rsid (where chromosomal positions exist)

Answer 1

[Elisabeth Gasteiger]

This file (humsavar.txt) is complemented by files of amino acid altering variants imported from Ensembl Variation databases. Mapped sequence variants are supplied per species in a tab delimited text file.ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/variants/

In particular, the human file is homo_sapiens_variation.txt.gz: The variants listed are the Ensembl Variation databases' set of 1000 Genomes project (http://www.1000genomes.org/) and Catalogue of Somatic Mutations In Cancer (COSMIC) v71, imported directly from COSMIC and via Ensembl Variation, protein altering variants (SO:0001583). COSMIC v71 variants are the last freely available somatic variants from COSMIC before their licence change; therefore the accuracy of the information provided for a COSMIC variant should be verified with COSMIC. (Text from README file in that directory)

Please don't hesitate to contact the UniProt helpdesk in case of questions about these files.

[arronslacey]

Thanks Elisabeth - very helpful! I had also looked into the Bisoconductor package VariantAnnotation that includes data objects such as polyPhen.Hsapiens.dbSNP131 - which maps most of the rsids to the humsavar dataset. it's obviously a bit out of date now so I much appreciate alternative data scourses that you mentioned.