Hi,
I have been analyzing the gene - BRAF
. I realized that this gene has a mutation which is present in both COSMIC
and dbSNP
.
For e.g.,
chr7 140453129
chr7 140481476
Both these single base mutations are present in COSMIC and dbSNP. In COSMIC these mutations are labeled as substitution_coding_silent
mutation
My understanding is that dbSNP has common mutations and COSMIC has mutations which are specific only for cancer. When I do variant analysis, I remove the common mutations, here dbSNP mutations and keep only COSMIC database mutations. But if I do this step now, I will be missing these mutations which are present in COSMIC.
Does anyone know why this occurs?
dbSNP is not a database of "common mutations". It now contains many sources of variation, some of which are not common. Also, there are MANY variants in dbSNP that are disease-associated, so I would not recommend using presence in dbSNP as a filter without a little extra work to pull out truly common variants.
Up-voted your question, though, as I'm glad you asked, and this seems to be a common misconception that many people have.