I am studying the consequences of transposable elements (TEs) in multiple S. cerevisiae populations. For this, I am using the web tool Variant Effect Predictor (VEP) from Ensembl. In the output, the number of overlapped genes is the same as for the overlapped transcripts, therefore my question is if VEP uses alternative splicing in their calculations to establish the number of transcripts? Otherwise, it seems that the same number of genes affected by the presence of a TE, is so for the transcripts which sound unlikely as I don't know, for instance, if the new variant is in an intron or in the stop codon which may produce an elongation of the transcript and during alternative splicing I can get multiple isoforms. I know VEP can give me more information about the consequence types, but it is just an idea of how the transcript could be affected by a TE being present in the gene, specifically. Or does VEP labels mRNA for the transcript that already had alternative splicing?
I hope you could help me out. Thank you in advance for your help.