2.2 years ago by
Republic of Ireland
These are the transcript splice isoforms of BRCA1, taken from UCSC Genome Browser. Different exons are transcribed in different isoforms.
When we describe a genetic variant using the standard nomenclature, we only provide chromosome, base position, ref allele, and alt allele. The only way that we can comprehensively annotate variants using this simple information is by annotating it for all known splice isoforms for the gene in which the variant is located.
Looking at the screenshot that I provide, you can appreciate that there are many regions in this gene where the variant would be in an exon and intron, depending on the splice isoform.
Additionally, in the human genome, there are many regions where 2 independent genes share overlapping sequence. In these cases, we have to annotate the variant for both genes, and their splice isoforms (if applicable).