Clarification on a 117-bp deletion variant DEL_CHR11_B8445432

Structural Variation
1

Hi,

I have a question regarding a 117-bp deletion variant designated DEL_CHR11_B8445432 in v4 and DEL_11_115846 in v2.
I have a case with a similar deletion, but ours is a 132-bp deletion with same rightside breakpoint; we initially called it a 117-bp deletion as well but upon further inspection, it looks like a 132-bp deletion with 15-bp microhomology (with some mismatches) at both ends.
I was wondering if you could please 1) assess whether DEL_CHR11_B8445432 is in fact a 132-bp deletion or 2) provide a BAM or CRAM file of a sample with this variant.

Thank you very much in advance.

Jaeseung Kim
University of Michigan

2

Hi Jaeseung,

Both ends of this deletion fall within simple repetitive sequences, where short-read alignments often struggle to accurately define breakpoints. If you have a sample carrying this event, I recommend reviewing the alignment patterns in IGV. If long-read data are available for that sample, those should provide additional clarity. Please note that we do not retain BAM files or release sample-level genotypes in gnomAD.

I hope this helps!