RTEL1 Intron 15 - Complex Region

General
1

I am reviewing some RTEL1 variants in intron 15 (c.1266+X) and wanted to clarify some things about a few entries.

  1. Based on my lab’s experience and reviewing the IGV reads in the following entries in gnomAD v4.1, can you confirm that the variants (within each class) are identical?

a. Deletions
i. 20-63685600-AGGGGCCACCTCCAGGAGGCAGGTGGAGGGCAGCCCTTGTTCCCCGGCAGGGCTGGGGGCCTTACAGTCCTATAAGGTG-A?dataset=gnomad_r4 (cannot put more than 2 links)
ii. gnomAD

b. Duplications
i. 20-63685600-A-AGGGGCCACCTCCAGGAGGCAGGTGGAGGGCAGCCCTTGTTCCCCGGCAGGGCTGGGGGCCTTACAGTCCTATAAGGTG?dataset=gnomad_r4 (cannot put more than 2 links)
ii. gnomAD

  1. Assuming the above deletions and above duplications are identical, do you know why intronic calls are being called as partially exonic and vice versa? Is this an issue with the alignment? Does it have to do with results from the forward strand versus the reverse strand?

Thanks in advance for your help!