Should mutations in repetitive base positions be considered real

Question

[tan]

Should mutations in repetitive base positions be considered real?

As far as I know, base repeat regions can cause inaccurate fluorescence signals obtained during the sequencing stage, resulting in false positives for insertions and deletions

I think my sequencing data also supports my point of view, as insertion and deletion occur simultaneously at the same location, which is quite rare in my experience.

But clinvar worries me because it marks this locus as pathogenic.NM_000059.4(BRCA2):c.2588del (p.Asn863fs)

To be honest, I'm a bit confused. I can't say 'all indels that occur in repeat regions are false positives', but based on my existing NGS sequencing data, I can't come to a better conclusion either.

Thank you for any suggestions

[Joe]

There may be better people here to answer this than me, but a few immediate reactions:

1. What kind of sequencing is it? Repeat effects are very technology-influenced - and related to this, what sequencing depth do you have that confirms vs contradicts that mutation?
2. That stretch doesn't look that repetitive to me to be honest. I think most current sequencing technologies can handle it reasonably well. Its following a different (C) base as well, so perhaps if it was toward the middle or the end of the stretch I'd be more inclined to doubt it.
3. Based on inferred tone, you seem surprised to see this particular mutation in this location - is there some added background here to give confidence to one answer over the other?