Variant nomenclature query

[Eva Tosco-Herrera]

Dear Mutalyzer team, 

I am a Ph.D. Student and I am currently in the process of submitting a manuscript to a scientific journal: Genetics in Medicine (https://www.journals.elsevier.com/genetics-in-medicine), specifically. This journal suggests checking variant nomenclature with Mutalyzer, and their guidelines ask authors to contact the respective software systems admin to resolve the errors or warnings prior to submitting the variant file. Hence, when I processed my variants with Mutalyzer, a few warnings showed up. I was wondering if you could help me solve these warnings, to accelerate the submission process. I would like to keep gene names in the variant nomenclature, so the reader can have a quick overview.

I attached the csv table with the warnings and their corresponding variants.

Thank you so much in advance.

Best regards,

Eva Tosco

Ph.D. Student -  Medical and Pharmaceutical Sciences

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Universidad de La Laguna

Avenida Astrofísico Francisco Sánchez, s/n.
Facultad de Ciencias. Apartado 456.
Código postal 38200
San Cristóbal de La Laguna. S/C de Tenerife

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Aviso de confidencialidad

[J.F.J. Laros]

Dear Eva Tosco-Herrera,

Thank you for using Mutalyzer.

The correct descriptions for these variants are (in order):

- NC_012920.1:m.3243A>G
- NM_001034853.2:c.2872del
- NM_001367250.1:c.1580_1582del
- NG_007466.2(NM_000314.4):c.493-5_528del
- NG_007110.2(NM_000251.2):c.366+1G>A

Any residual warnings are only there to inform the user that effect predictions
should not be trusted because the variant in question probably affects
splicing.

Because genes can have multiple transcripts, the HGVS dropped [1] the use of
gene symbols. The new version of Mutalyzer [2] correctly handles this.

I hope this helps.


With kind regards,
Jeroen.

References:
[1] https://varnomen.hgvs.org/bg-material/refseq/
[2] https://v3.mutalyzer.nl

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