Question related to CNV nomenclature using seq[GRCh37]

Sarantaus, Laura X

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Feb 5, 2025, 3:35:55 AMFeb 5

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Dear Sir/Madam,

I would like to ask if it is based on the HGVS nomenclature that for example in gross deletions that affect only one cytoband, you have to put initial cytoband and final cytoband, so that the band comes twice in the name (both initial and final cytoband are the same).

For example:

seq[GRCh37] del(15)(q15.3q15.3), chr15:g.43891794_43941146del, is right, and the following is not:

seq[GRCh37] del(15)(q15.3), chr15:g.43891794_43941146del

I was not able to find an answer to this question from the HGVS website.

Best, Laura Sarantaus

PhD, Geneticist

Blueprint Genetics

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Ros Hastings

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Feb 7, 2025, 12:55:53 AMFeb 7

to Sarantaus, Laura X, hgvs-nom...@googlegroups.com

Dear Laura

ISCN 2024 has the updated ISCN/HGVS nomenclature. For the karyotype like ISCN you need to put both breakpoints in to show it is an interstitial loss but not for the array(sequence)like nomenclature as the nucleotides show you it it interstitial. So depending on which platform is being used you would write either.

seq[GRCh37] del(15)(q15.3q15.3)

NC_000015.9:g.43891794_43941146del

or

seq[GRCh37] 15q15.3(43891794_43941146)x1

NC_000015.9:g.43891794_43941146del

The HGVS website will be updated in due course. In the meantime then the combined nomenclature is available on ISCN – Interpretation & communication of human cytogenomic nomenclature / Home (https://iscn.karger.com)

seq[GRCh37] del(15)(q15.3q15.3), chr15:g.43891794_43941146del, is not correct.

I hope this helps

Kind regards

Ros

Ros Hastings

GenQA Consultant

ISCN Standing Committee Chair

Oxford University Hospitals NHS Trust

Oxford

Kind regards

Ros

Ros Hastings

GenQA Consultant

ISCN Standing Committee Chair

Oxford University Hospitals NHS Trust

Oxford

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Johan den Dunnen

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Feb 7, 2025, 1:47:34 PMFeb 7

to HGVS Nomenclature

Dear Laura,

in addition to the reply above, please note the description NC_000015.9:g.43891794_43941146del implies the breakpoint of the deletion has been sequenced. When this is not the case, correct is NC_000015.9:g.(?_43891794)_(43941146_?)del. Of course the "?" positions can be specified when you know sequences outside the deleted region.