get rsID or positions from variant name/gene info

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4.0 years ago

Floydian_slip ▴ 170

Hi, I have a list of variant and gene info as follows:

MCOLN1  c.406-2A>G
G6PC    c.247C>T
PCDH15  c.733C>T
CLRN1   c.144T>G
NEB     c.7431+1917_7536+372del

I would like to either get rsIDs or preferably their coordinates in hg19/GRCh37. Is there a straight forward way of doing this? I have 100s of such entries hence manually not possible. Thanks so much in advance.

clinvar dbSNP rsID variants • 1.2k views

ADD COMMENT • link 4.0 years ago by Floydian_slip ▴ 170

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Past threads that may be useful:
Genomic coordinates from traditional HGVS variants
Retrieve mutation position and ID for a mutation in hgvs format

https://mutalyzer.nl/position-converter
https://variantvalidator.org/

ADD REPLY • link 4.0 years ago by GenoMax 147k

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Thanks, genomax! This is helpful. However, I was wondering if there is any tool which will not need the transcript info? Both these tools do. I know it sounds weird to list the coordinates of these variants without the transcript info but unfortunately that's all I have from a collaborator.

ADD REPLY • link 4.0 years ago by Floydian_slip ▴ 170

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