batch variant validation by Name Check

[Qin Zixin]

Hi, 

I am currently submitting to Genetics in Medicine and I have used your database to ensure that my variants are conform to current HGVS nomenclature. Unfortunately, I have some warning messages for my variant as attached excel file marked as yellow. Can you please confirm that these variants are correct or tell me how to correct it? 

Thanks a lot.

 

Best regards,

 

Zixin Qin

 

[Mihai Lefter]

Dear Zixin Qin,

Thanks for using Mutalyzer.

Some of your descriptions have been corrected by Mutalyzer. In your particular case, you can check which ones by comparing columns E and G. For example, for the input description "NC_000013.11(NM_000059.3):c.*1828_*1834del", by looking at column G, the corrected description is "NC_000013.11(NM_000059.3):c.*1836_*1842del".

Best regards,

Mihai

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[Qin Zixin]

Hi Mihai,

 

Thank you for reply.

Then may I ask you how about the variant with error info about affecting splice region, is the describtion correct? Such as the variant “NC_000017.11(NM_007294.3):c.-235A>G with error ‘ (GenRecord): Mutation near splice site in gene BRCA1 transcript 002 (selected).|(GenRecord): Mutation near splice site in gene BRCA1 transcript 003.”.  Should I do anything for these kind of variant?

Thank you.

 

Best regards,

Zixin

[Qin Zixin]

Hi, Mihai,

 

And also, actually my variants input was converted based on their position change in vcf file through the Mutlyzer position converter, however, when validating the variant with NameChecker, it showed error. For these situation, is the result from position converter correct? And which description should I use?

 

Thanks a lot.

 

Best regards,

 

Zixin

 

From: Mihai Lefter <mihai....@gmail.com>

Date: Monday, September 12, 2022 at 21:19
To: Qin Zixin <yb8...@connect.um.edu.mo>
Cc: muta...@googlegroups.com <muta...@googlegroups.com>
Subject: Re: [mutalyzer] batch variant validation by Name Check

[Mihai Lefter]

Hi Zixin,

The results from the NameChecker should be used. In addition, the "mutation near splice site" message is only there as additional information for the user.

Best regards,

Mihai

[Qin Zixin]

So the description of the variants with warnings “ mutation/variant near splice site …” are correct that no need to change, right?

 

zixin

[Mihai Lefter]

Dear Zixin,

Please perform the steps mentioned in my first reply for all the variants because there could be the "mutation" warning for variants that are corrected by the NameChecker.

Best regards,

Mihai