hgvs

[Ver...@seznam.cz]

Good morning,

I would like to ask what the correct notation is for reporting 2 variants in thrombophilia testing. Is for example 

NM_000130.5:c.[1601G>A];[1601=] p.[(Arg534Gln)];[Arg534=];NM_000506.5:c.[*97=];[*97=]

correct?

Thank you and have a nice day!

[Johan den Dunnen]

Dear Verca,

before I can answer your question, I need more information. Are the variants 

following HGVS nomenclature recommendations (see also https://hgvs-nomenclature.org/stable/recommendations/DNA/alleles/), a correct description is NM_000130.5:c.[1601G>A;*97=];[1601=;*97=] p.[(Arg534Gln)];[Arg534=].

Best regards,

Johan den Dunnen
HUGO HGVS Variant Nomenclature Committee (HVNC)

Op maandag 14 juli 2025 om 13:18:05 UTC+2 schreef Ver...@seznam.cz:

[Fokkema, I.F.A.C. (HG)]

Dear Johan,

It's possible that your email was sent before it was finished, as it
seems to contain an unfinished sentence. Either way, since two
different reference sequences are used, your given example description
is not correct.

NM_000130.5:c.[1601G>A];[1601=] p.[(Arg534Gln)];[Arg534=]

and

NM_000506.5:c.[*97=];[*97=]

can not be contracted into just using NM_000130.5.


It is actually under debate whether the allele syntax can be used for
multiple reference sequences. This remains to be an open issue:
https://github.com/HGVSnomenclature/hgvs-nomenclature/issues/170

However, since these variants lie even on different chromosomes, they
can not share an allele, and can not be contracted into one
description. The descriptions should, therefore, be kept separate.

Regards,

Ivo

[Johan den Dunnen]

Dear Ivo,

you are right, I missed that two different reference sequences were used.

Since the reference sequence link to different chromosomes, the variants can not be combined into one allele description. Following HGVS nomenclature, I indeed get to what you suggest, i.e. NM_000130.5:c.[1601G>A];[1601=] p.[(Arg534Gln)];[Arg534=]NM_000506.5:c.[*97=];[*97=], to describe the variants detected.

Best regards,

Johan den Dunnen
HUGO HGVS Variant Nomenclature Committee (HVNC)

Op donderdag 28 augustus 2025 om 14:09:22 UTC+2 schreef i.f.a.c...@gmail.com: