I am returning to bioinformatics after a long absence and the landscape has certainly changed and there are a few (well, a lot of) things I'm not clear about.
Taking the human genome as an example, what is the difference between a SNP and an entry in a the HGMD? I've been using the ensembl genome browser to look at sequence variations and I'm unsure as to why some are classed as SNPs and some mutations. My understanding of a SNP is that it is a mutation that happened a long time ago and has now become established as a polymorphism in the population, so you refer to it as a polymorphism not a mutation. Using that logic a mutation would be a a variation from the reference genome which has recently occured, but I don't think that's the right answer. I think a mutation is a SNP associated with a disease phenotype. However SNPs and HGMD mutations that cause missense mutations seem to be treated differently by ensembl and I don't understand why and it is confusing me.
Take this example gene and transcript Gene: ENSG00000163914 Transcript: ENST00000296271
There is a 'mutation' at the 4th codon which gives rise to a missense mutation and is linked to the HGMD via this ID: CM930647. However this mutation is not listed among the protein variants for this transcript. Other variants from SNPs and some other mutations are listed. Perhaps this is nothing more than an error in the database.
Thanks in advance for your help