search

macarthur-lab / gnomad_browser

gnomAD browser pre-ASHG 2018
MIT License
33 stars 16 forks source link

Missing dbSNP RS ID #128

Closed lonphan closed 3 years ago

lonphan commented 6 years ago

Hi,

I'm following up with a user of dbSNP and ExAC for a question as to why some ExAC variants don't have RS ID. For example this variant. http://exac.broadinstitute.org/variant/22-46594255-G-A

dbSNP have released RS IDs for all GnomAD and ExAc variants in latest build 151. For the variant above the RS ID is rs769784767. https://www.ncbi.nlm.nih.gov/snp/rs769784767

Can ExAC browser be updated to include the new RS ID? There's an API to get the matching RS ID. Exac variant: 22-46594255-G-A Converted to SPDI format: NC_000022.10:46594255:G:A

curl -X GET --header "Accept: application/json" "https://api.ncbi.nlm.nih.gov/variation/v0/spdi/NC_000022.10%3A46594254%3AG%3AA/rsids"

The complete list of corresponding chromosome accessions for GRCh37 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25)

Otherwise, please contact snp-admin@ncbi.nlm.nih.gov if you need help getting the complete list of RS IDs.

nawatts commented 3 years ago

We do not continuously update the dbSNP rsIDs displayed in the browser, so there will be some differences the databases and dbSNP depending on versions been used. ExAC was annotated with dbSNP version 141.

See the "Why is this variant linked to the wrong dbSNP rsID?" FAQ entry.