Warning-splice site variants

[Kimberly Coetzer]

Hello, 

I need some advice.

I am trying to verify some mutations using Mutalyzer. I have some splice site variants that give a warning.

Input: NC_000011.9(NM_002599.4):g.72289940C>T

Output warning: Mutation on splice site in gene PDE2A transcript 001.

I see from previous comments that warnings mean that the description is correct but caution should be taken with interpretation.

This data needs to be published and we are worried about getting a rejection because of the warning message on the variant.

Is the variant description good enough for publication even when there is a warning? 

Thank you in advance.

Kind regards

Kimberly

[J.F.J. Laros]

Dear Kimberly,

A warning indeed merely indicates that caution is advised when interpreting the
effect of the variant, i.e., RNA and protein predictions.

Your description is a bit peculiar however, since you select a transcript in
combination with genomic coordinates. It should be simplified to:

NC_000011.9:g.72289940C>T

as Mutalyzer suggests in the section "Genomic description. If you want to
describe this variant relative to the transcript, the following description
should be used:

NC_000011.9(NM_002599.4):c.2469+1G>A

I hope this helps.


With kind regards,
Jeroen.

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