Question regarding deletions beyond the transcribed region

Bosscher, L (medgen)

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Jan 27, 2026, 9:10:24 AMJan 27

to hgvs-nom...@googlegroups.com, Poppema-de Jong, EJ

Dear HGVS committee,

We are a diagnostic laboratory from the UMCG (University Medical Center of Groningen) in the Netherlands.

We want to describe the deletions and duplications according to the HGVS Nomenclature general "exon-based" description.

This works well for most duplications/deletions, but we don't know how to describe duplications/deletions that lie outside the transcribed region.

We have attempted to describe the SMN1 deletion exons 7 & 8 using the general "exon-based" description.

We arrive at the following:

(723+1_724-1)_(*1_*4-1) del p.? NM_000344.4 GRCH37(hg19). Systemic numbering

Another example is deletion exons 4 through 10 in the IKBKG gene, which arrives at:

(399+1_400-1)_(*1_*572-1) del p.? NM_001099857.5 GRCH37(hg19). Systemic numbering

Under the heading "deletions extending beyond the transcribed region," we saw that the HGVS nomenclature committee is discussing whether a c.-based format should be proposed.

We're wondering if you already know more about this.

And if you could help us with the correct HGVS nomenclature of both deletions mentioned here above?

Thank you very much in advance,

Kind regards,

Laura Bosscher

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Johan den Dunnen

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Jan 30, 2026, 11:01:32 AMJan 30

to HGVS Nomenclature

Dear Laura,

following current HGVS nomenclature, variants must be described at a genomic level, descriptions at other levels may be added.

- the first variant is described as NC_000005.10:g.(70944754_70946065)_(70951995_70952438)del NM_000344.3:c.(723+1_724-1)_(*3+1_*4-1)del. Note that when you use an "exon-based" description "(*1_*4-1)" is not correct.

- the second variant is described as NC_000023.11:g.(154556377_154558531)_(154565033del_?)del NM_001099857.5:c.(399+1_400-1)_(*572_?)del. Note again that for an "exon-based" description "(*1_*572-1)" can not be used (both position are not flanking an exon). For the description I assumed the 3'end of the deletion extends beyond the reference transcript.

> Under the heading "deletions extending beyond the transcribed region," we saw that the HGVS nomenclature committee

> is discussing whether a c.-based format should be proposed.

In my reply I assumed the c.format will be allowed for deletions extending beyond the transcribed region.

Best regards,

Johan den Dunnen
HUGO HGVS Variant Nomenclature Committee (HVNC)

Op dinsdag 27 januari 2026 om 15:10:24 UTC+1 schreef Bosscher, L (medgen):

Bosscher, L (medgen)

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Mar 24, 2026, 9:44:14 AM (9 days ago) Mar 24

to hgvs-nom...@googlegroups.com

Dear HGVS committee,

We have seen your response to the email below in the HGVS nomenclature conversation groups, thank you for that.

We have been working on it and do have a question for clarification.

We wonder why, with the “exon based” notation, the position for SMA is determined after the UTR, whereas for IKBKG it concerns the last base of the UTR.

We would like to hear more about the considerations behind this choice.

Kind regards,

Laura Bosscher

Johan den Dunnen

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Mar 30, 2026, 8:53:46 AM (3 days ago) Mar 30

to HGVS Nomenclature

Dear Laura,

not sure what you mean. Following HGVS nomenclature (see the Uncertain page, hgvs-nomenclature.org/stable/recommendations/uncertain/), the description should be based on the probes used in the assay to detect the variant. I simply replied to the example descriptions you gave. I have no clue what assay was used so can not comment on the fact whetehr the descriptions are OK.