Question about damaging/deleterous effect of SNP - is it visible in IGV?

[SaulGoodman]

Hello all together,

I have a question that explicitly refers to a SNP that is calculated to have a damaging/deletious effect.

Now I ask myself whether this effect should also be seen in the IGV? It is exactly this SNP (https://varsome.com/variant/hg38/chr2-165315571-C-T?).

Can anyone give me tips on how to track down the SNP and tell me more precisely whether the calculations are correct?
I have the sample in front of me, a screenshot is attached.

And if I should be completely on the wrong track I would also like to know why. I want to learn

I thank you in advance to everyone who gives me an answer here.

 

Edited July 17, 2023 by SaulGoodman
edit