Variant nomenclature in clinical reports

Teresa Imizcoz

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Jun 4, 2026, 4:30:29 AMJun 4

to HGVS Nomenclature

Dear HGVS team,

I work as a variant curator in a diagnostic lab and we have run into a question regarding variant nomenclature in clinical reports.

Following HGVS recommendations this is the nomenclature we have been using: EGFR (NM_005228.5):c.2156G>C p.(Gly719Ala)

We participate in several EMQN schemes and we have recently got this observation: "HGVS Nomenclature does not use ( ) brackets for the transcript reference sequence except when a genomic reference sequence is included first" and the suggested nomenclature recommendation was as it follows: EGFR NM_005228.5:c.2156G>C p.(Gly719Ala)

Going through the recommendations on the website we do see that brackets are used for transcript identifier if NG_ is included:
Genome reference with coordinates from aligned transcript_
Syntax sequence_identifier "(" transcript_identifier "):c." transcript_position reference_sequence ">" alternate_sequence
Examples: NG_012232.1(NM_004006.2):c.93+1G>T

However, gene symbol/name is not included and yet helpful for clinicians when it comes to clinical reports.

If included, where should the gene symbol go? before or after transcript identifier? should brackets ( ) be used for either gene symbol or transcript identifier? What should the correct nomenclature be?:
EGFR (NM_005228.5):c.2156G>C p.(Gly719Ala)
EGFR NM_005228.5:c.2156G>C p.(Gly719Ala)
NM_005228.5 (EGFR):c.2156G>C p.(Gly719Ala)

Does it make any difference?

Thanks in advance for your help

Kind regards

Johan den Dunnen

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Jun 9, 2026, 8:56:07 AMJun 9

to HGVS Nomenclature

Dear Teresa,

following HGVS variant nomenclature the correct description of the variant is "NC_000007.14:g.55174015G>C NM_005228.5:c.2156G>C p.(Gly719Ala)".

Note that HGVS demands that "all variants should be described at the most basic level, the DNA level. Descriptions on the RNA and/or protein level may be given in addition", see Geneneral recommendations.

Furthermore, HGVS does not allow the addition of gene symbols in variant nomenclature, so "EGFR (NM_005228.5):c.2156G>C" should not be used. When you want to include the gene symbol, you could e.g. use "EGFR NC_000007.14:g.55174015G>C NM_005228.5:c.2156G>C p.(Gly719Ala)".

Best regards,

Johan den Dunnen
HUGO HGVS Variant Nomenclature Committee (HVNC)

Op donderdag 4 juni 2026 om 10:30:29 UTC+2 schreef Teresa Imizcoz:

Teresa Imizcoz

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Jun 10, 2026, 2:07:09 PMJun 10

to HGVS Nomenclature

Dear Johan,

Thanks for your prompt response.

Is there any other way to include this information in order to make it more easily readable and understandable for clinicians and patients?

Our goal is to write reports following HGVS guidelines but we also need the information to be clear for clinicians. Could NC_/NM_ information be included in the report somehow (methodology) and the variant information display in a simplified table with cDNA and protein level descriptions?

Thank you for clarifying this. We are doing our best to find a balance between understandable and correct/complete reports

Regards

Teresa Imizcoz

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Jun 10, 2026, 2:07:12 PMJun 10

to HGVS Nomenclature

Dear Johan,

Thanks for your prompt response.

Regards,

Teresa

El martes, 9 de junio de 2026 a las 14:56:07 UTC+2, Johan den Dunnen escribió:

Teresa Imizcoz

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Jun 22, 2026, 7:19:19 AM (5 days ago) Jun 22

to HGVS Nomenclature

Sorry to insist on this topic. We found the recommendations a bit difficult to implement in a clinical context. I copy my last email to see if we can get a reply

Dear Johan,

Thanks for your prompt response.

Is there any other way to include this information in order to make it more easily readable and understandable for clinicians and patients?

Our goal is to write reports following HGVS guidelines but we also need the information to be clear for clinicians. Could NC_/NM_ information be included in the report somehow (methodology) and the variant information display in a simplified table with cDNA and protein level descriptions?

Thank you for clarifying this. We are doing our best to find a balance between understandable and correct/complete reports

Regards

Johan den Dunnen

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Jun 22, 2026, 9:07:36 AM (5 days ago) Jun 22

to HGVS Nomenclature

Dear Teresa,

HGVS nomenclature has been designed to unequivocally describe variants in DNA, RNA and protein sequences. To prevent mistakes and confusion the official dewcription is indeed rather complex. People who do not understand the code shoudl not use it. HGVS nomenclature exists since 2000, that's over 25 years. Since they need to understand HGVS noemnclature, it should be part of the basic training of clinicians. What, besides the official description, you want to add to your report for e.g. patients/families to understand the DNA change(s) found, is up to you.