Question: Differences in Cosmic Id, dbSNP Id and Coding change for a gene
0
gravatar for sumirp77
3.1 years ago by
sumirp770
sumirp770 wrote:

Hi All,

I recently analyzed a sample in Ion reporter for CHP and the data I got had the usual annotations like gene, location, coding ,amino acid change,etc etc.Herein I observed that for a particular gene the variant (coding change) i got was not matching with the Cosmic Id and dbsnp id annotated with the gene. So I can I decide which info is important.

Thanks

sequencing snp gene • 1.4k views
ADD COMMENTlink modified 3.1 years ago by Denise - Open Targets5.0k • written 3.1 years ago by sumirp770

Do you mean that the amino acid change wasn't matching the amino acid change listed for the accompanying dbSNP ID and COSMIC IDs? I'm not sure how Ion Reporter does its annotations. As @Denise pointed out you could be looking at annotations for the wrong reference build. Also if Ion Reporter isn't doing exact matching you can have multiple dbSNP and COSMIC IDs that overlap a given position that map to different specific nucleotide changes so it could be reporting the wrong ID.

ADD REPLYlink written 3.1 years ago by Dan Gaston7.1k
1
gravatar for Denise - Open Targets
3.1 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

Why did you expect this variant to match to a COSMIC or dbSNP ID? It may be a novel variant, never described before? Or your data is in one assembly (e.g. GRCh37 or hg19) and you are now looking at GRCh38? See this post for more details on the differences between them two. Be sure which assembly your data is on and try the Ensembl VEP to annotate your variants and tell you whether they are novel or existing.

ADD COMMENTlink written 3.1 years ago by Denise - Open Targets5.0k
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