Error for intronic variants in mutalyzer

[Lai, Abbe]

Dear Mutalyzer team,

 

I received an error message for the intronic variants in a batch name checker job. I am sure that they follow HGVS nomenclature to denote intronic variants. I also including the NM number as the tip in the output suggests. I am not sure why I am receiving these errors.

 

Any information you could provide for this would be extremely helpful.

 

Thank you.

Best,

Abbe Lai, MS, CGC

Licensed Genetic Counselor

Coordinator, Brain Development and Genetics Clinic

Research Coordinator, Walsh Laboratory

Abbe...@childrens.harvard.edu

617-919-4371 | fax 617-919-2300 www.walshlab.org

 

 

 

[J.F.J. Laros]

Dear Abbe Lai,

Thank you for using Mutalyzer.

It is not possible to describe intronic variants using a transcript reference
sequence because these reference sequences do not contain introns. A genomic
reference sequence should be used instead.

For example, the following description is incorrect:

NM_004006.2:c.357+1G>A

But this one is correct:

NC_000023.10(NM_004006.2):c.357+1G>A

Please see the HGVS nomenclature pages [1] for more information.


References:
[1] https://varnomen.hgvs.org/bg-material/refseq/

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Jeroen F.J. Laros - J.F.J...@lumc.nl