Dear all,
How to find the rs(number) if I have the SNP and allele, for example; what is the rs(number) of Gene: NPC1L1, 1735 C>G, C/C ?
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fatma.mokhtar •
first convert to genomic position Amino Acid Change To Genomic Location and then convert the position to a rs: Get rs number based on position
I would change it into HGVS format then use it as input for the VEP. You may experience some problems using gene names as HGVS input, because it really requires something more specific like a versioned transcript or protein identifier. If you just give it a gene name it will assume the Ensembl canonical transcript, which may not be the transcript you mapped against. This blog post talks about how the VEP deals with HGVS ambiguity in terms of proteins, but the stuff about transcript choice applies when you're using nucleotide changes too.
You have to be more specific. Such as: Chromosome # Position #
or give the cDNA change.
rs(number) also known as rsids can be found in dbSNP database.
This is a SNP in Meada. T, article; https://www.ncbi.nlm.nih.gov/pubmed/20379057 I couldn;t find the rs
Hello, So, here is the thing. This paper got that mutation or variant from another paper and it keeps referencing it more than once. When I checked that paper it mentioned the gene and the multiple variants and dbsnp or rsid of the mutation in question.
https://onlinelibrary.wiley.com/doi/full/10.1111/j.1399-0004.2004.00388.x
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A listing of all variants in this gene in a tabular format from Ensembl.