HGVS nomenclature of DNA substitution resulting in an exon deletion

[Grootscholten, PM (medgen)]

Dear collegue,

 

Could you provide me with the just HGVS nomenclature of a DNA substitution resulting in an exon deletion?

In this case we have a LIPA substitution c.894G>A p.= (NM_000235.4) resulting in a deletion of exon 8 (p.(Ser275_Gln298del)).

What will be the correct HGVS nomenclature of this variant?

 

Remain with c.894G>A p.=

Or c.894G>A p.(Ser275_Gln298del)

Or r.823_894del p.(Ser275_Gln298del) (for us in presymptomatic DNA testing this is difficult because you don’t see what variant change you have to consider).

Or a combination?

 

Thank you so much for informing me in advance!

 

Petra Grootscholten
| Stafanaliste i.o. | Genoomdiagnostiek | Genetica | UMCG |

| Antonius Deusinglaan 1 | 9713 AV Groningen |
| 5e verdieping | Huispostcode CB50 |
| tel: 06-52724907 (68475) |e-mail: p.m.groo...@umcg.nl (afwezig op donderdag) |

 

 

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[Johan den Dunnen]

Dear Petra,

following HGVS nomenclature the variant shold be described as NC_000010.11:g.89222511C>T NM_000235.4:c.894G>A r.(823_894del) p.(Ser275_Gln298del). This description assumes you did not analyse RNA but take the effect on RNA level from another study. When you did analyse RNA you can remove the parentheses from the description.

Best regards,

Johan den Dunnen
HUGO HGVS Variant Nomenclature Committee (HVNC)

Op vrijdag 7 november 2025 om 10:59:58 UTC+1 schreef Grootscholten, PM (medgen):

[Grootscholten, PM (medgen)]

Dear collegue,

 

I am sending you my email again, because I didn’t receive an answer yet.

This is just a reminder.

 

Thank you for looking into this.

Petra Grootscholten

[Johan den Dunnen]

Dear Petra,

your question has been answered, please see above (https://groups.google.com/g/hgvs-nomenclature/c/TsqXTVgm4_8).

Best regards,

Johan den Dunnen
HUGO HGVS Variant Nomenclature Committee (HVNC)

Op maandag 24 november 2025 om 10:36:46 UTC+1 schreef Grootscholten, PM (medgen):