Can the UCSC browser be used to predict the effect of novel SNPs on a transcript (e.g. synonymous and non synonymous)? I was wondering if UCSC did any 'processing' on novel snps (e.g. looked to see what transcripts they might be in and find the consequences) or whether it looked for intersection with existing SNPs in the database and just reported the consequences of those SNPs already in the database. Or perhaps it does neither of those.
I have seen the SNP analysis tool ANNOVAR claim that it can annotate novel SNPs but this tool is based on the UCSC browser tracks. I was wondering if the ability to handle novel SNPs is written into the UCSC browser or whether ANNOVAR has added an additional annotation layer to supplement the UCSC information.