For reverse genes, why is there a difference in the deletion in genomic and transcript annotation? Why is the deletion in a repeat region displayed incorrectly?

Alamut^TM Visual Plus applies the internationally recognized HGVS nomenclature. In the case of reverse genes, the 3’ rule is applied. For all descriptions, the most likely 3’ position of the reference sequence is arbitrarily assigned to have been changed. The 3’ rule also applies to changes in single residue stretches and tandem repeats (nucleotide or amino acid). The 3’ rule applies to ALL descriptions (genome, gene, transcript, and protein) of a given variant. See: http://varnomen.hgvs.org/recommendations/general/