Doubt

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MARIA GARCIA BARCINA

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Aug 12, 2024, 11:56:56 AM8/12/24

to hgvs-nom...@googlegroups.com, ALEJANDRO JOSE RAVELO MARRERO

Dear colleagues,

A few years ago we found a variant in MSH2 gene that we called (NM_000251.2:c.2634G>A /NP_000242.1:p.Gly820Alafs*3), which corresponds to rs63751624, and would be synonymous. However, the RNA studies published by Pérez Carbonero showed an exon15 deletion. Our question is if we should continue naming it as synonymous or should we take into account the exon skipping caused.

Thank you very much for your collaboration,

María

Dra. María García Barcina

Genetikako Unitatea/Unidad de Genética

Bilbo-Basurtu ESI/ OSI Bilbao-Basurto

Montevideo Etorbidea / Avda. Montevideo, 18

48013-BILBAO (Bizkaia)

( 94.400.6128

Johan den Dunnen

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Aug 15, 2024, 2:19:49 AM8/15/24

to HGVS Nomenclature

Dear Maria,

from the HGVS nomenclature website (see https://hgvs-nomenclature.org/stable/recommendations/general/): "when listing variant types, HGVS recommends listing them separately for each level, i.e. DNA, RNA, and protein". It seems that in the case you describe you identified on DNA level a substitution, on RNA level a deletion, and on protein level a frameshift. Note that HGVS nomenclature does not use the term "synonymous" but it seems that based on the publication you mention, you can not call this variant "synonymous".

Best regards,

Johan den Dunnen
HUGO HGVS Variant Nomenclature Committee (HVNC)
http://www.HGVS.org/varnomen