This is a very interesting edge case caught by fuzz test. We always represent any variant in a form of substituion. For deletion, we usually include a nucleotide before the deleted sequence. For example for the transcript sequance below, a deletion of AAAAAAA is represented as a substitution from GAAAAAAA -> G.
ATGAAAAAAATTTT
But if the start of the deletion (the first A) happens to be the nucleotide after start codon, we use the end inclusion format of AAAAAAAT -> T.
So this edge case is when the last A is the end of an exon. The T then becomes the start of the next exon. Variant coordination did not handle this properly. We should still be able to handle this variant.
This is a very interesting edge case caught by fuzz test. We always represent any variant in a form of substituion. For deletion, we usually include a nucleotide before the deleted sequence. For example for the transcript sequance below, a deletion of AAAAAAA is represented as a substitution from GAAAAAAA -> G.
ATGAAAAAAATTTT
But if the start of the deletion (the first A) happens to be the nucleotide after start codon, we use the end inclusion format of AAAAAAAT -> T.
So this edge case is when the last A is the end of an exon. The T then becomes the start of the next exon. Variant coordination did not handle this properly. We should still be able to handle this variant.