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HGVS Nomenclature
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Charlie Rowlands
,
Johan den Dunnen
2
Apr 18
HGVSp nomenclature for pseudoexon-induced amino acid insertions
Dear Charlie, to understand your question, please base it on an exact variant description incl. a
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HGVSp nomenclature for pseudoexon-induced amino acid insertions
Dear Charlie, to understand your question, please base it on an exact variant description incl. a
Apr 18
Depienne, Christel
,
Johan den Dunnen
2
Apr 17
Nomenclature of a variant associated with leaky splicing (production of two mRNA/protein isoforms)
Dear Christel, regarding your question, please first note that NM_003491.4(NAA10):c.342-9C>A) is
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Nomenclature of a variant associated with leaky splicing (production of two mRNA/protein isoforms)
Dear Christel, regarding your question, please first note that NM_003491.4(NAA10):c.342-9C>A) is
Apr 17
Marta Vila
, …
Johan den Dunnen
4
Apr 16
reason for intronic nomenclature
Thanks! Sincerely, Marta O luns, 15 de abril de 2024 á/s 11:05:54 UTC+2, jtden...@gmail.com escribiu:
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reason for intronic nomenclature
Thanks! Sincerely, Marta O luns, 15 de abril de 2024 á/s 11:05:54 UTC+2, jtden...@gmail.com escribiu:
Apr 16
CHU, Sin I (BIRMINGHAM WOMEN'S AND CHILDREN'S NHS FOUNDATION TRUST)
, …
i.f.a.c...@lumc.nl
4
Apr 16
complex HGVS enquiries.
Dear all, Note that since the HGVS nomenclature has no rules for prioritizing insertions that contain
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complex HGVS enquiries.
Dear all, Note that since the HGVS nomenclature has no rules for prioritizing insertions that contain
Apr 16
Cetty Santonocito
, …
i.f.a.c...@lumc.nl
4
Apr 15
intronic variant
> A description like NM_007294.4:c.5216_5278-2751del could be correct, > and it indicated that
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intronic variant
> A description like NM_007294.4:c.5216_5278-2751del could be correct, > and it indicated that
Apr 15
Laura Jentsch
,
Johan den Dunnen
2
Apr 15
legal clarification
Dear Laura, the recommendations for the description of sequence variants, the so called "HGVS
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legal clarification
Dear Laura, the recommendations for the description of sequence variants, the so called "HGVS
Apr 15
ARIANNA VENTRELLA
,
Johan den Dunnen
2
Apr 15
HGVS nomenclature for no disease associated variant detection
Dear Arianna, HGVS nomenclature was developed to describe variants, not to write a diagnostic report.
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HGVS nomenclature for no disease associated variant detection
Dear Arianna, HGVS nomenclature was developed to describe variants, not to write a diagnostic report.
Apr 15
María García Hoyos
,
I.F.A.C...@lumc.nl
2
Mar 25
Extension variants
Dear María, Extension variants are only described as such when the protein sequence is only extended,
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Extension variants
Dear María, Extension variants are only described as such when the protein sequence is only extended,
Mar 25
Xin Chen
, …
I.F.A.C...@lumc.nl
3
Mar 25
Question: convert minimized deletion/insertion alleles
Dear Xin, Note that also, the notation for the insertion is ambiguous. The deletion is clear,
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Question: convert minimized deletion/insertion alleles
Dear Xin, Note that also, the notation for the insertion is ambiguous. The deletion is clear,
Mar 25
Harri Webb
,
Johan den Dunnen
3
Mar 7
Nomenclature query for a variant downstream from a frameshift variant
Dear Johan, Thank you very much for the clarification. Harri On Monday 29 January 2024 at 23:17:15
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Nomenclature query for a variant downstream from a frameshift variant
Dear Johan, Thank you very much for the clarification. Harri On Monday 29 January 2024 at 23:17:15
Mar 7
MAVRAKI, Eleni (THE NEWCASTLE UPON TYNE HOSPITALS NHS FOUNDATION TRUST)
,
Johan den Dunnen
2
Mar 1
Nomenclature help regarding consecutive changes
Dear Elena, the current HGVS nomenclature recommendations (see https://hgvs-nomenclature.org/stable/
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Nomenclature help regarding consecutive changes
Dear Elena, the current HGVS nomenclature recommendations (see https://hgvs-nomenclature.org/stable/
Mar 1
Magdaléna Dvořáková
,
Johan den Dunnen
4
Mar 1
Mitochondrial DNA
Dear Magdalena, following HGVS nomenclature, the format to use is NC_012920.1:m.8379A>G and
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Mitochondrial DNA
Dear Magdalena, following HGVS nomenclature, the format to use is NC_012920.1:m.8379A>G and
Mar 1
Marija Terzikj
,
Johan den Dunnen
2
Mar 1
Reporting only 2 tested variants
Dear Marija, based on the HGVS nomenclature, see https://hgvs-nomenclature.org/stable/recommendations
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Reporting only 2 tested variants
Dear Marija, based on the HGVS nomenclature, see https://hgvs-nomenclature.org/stable/recommendations
Mar 1
Åberg Kristin
,
Johan den Dunnen
2
Mar 1
Nomanclature of two insertions separated by 3 bases
Dear Kristin, since both variants affect the reading frame but together have no effect on it, best
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Nomanclature of two insertions separated by 3 bases
Dear Kristin, since both variants affect the reading frame but together have no effect on it, best
Mar 1
Ewa Szymanek
,
Johan den Dunnen
2
Feb 26
Dear Ewa, it seems you spotted a typo, thanks for pointing it out. Correct is NP_003997.1:p.(Ser73Arg
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Dear Ewa, it seems you spotted a typo, thanks for pointing it out. Correct is NP_003997.1:p.(Ser73Arg
Feb 26
Maria Vila Casadesús
,
Johan den Dunnen
2
Feb 26
Nomenclature - gene fusion
Dear Maria, the format you give, NM_153649.4:r.?_664::NM_002529.4:r.1196_?, can only be used to
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Nomenclature - gene fusion
Dear Maria, the format you give, NM_153649.4:r.?_664::NM_002529.4:r.1196_?, can only be used to
Feb 26
Steven Roels
,
Johan den Dunnen
4
Feb 26
Notation for multi-amino-acid silent mutations
Dear Steve, indeed, following HGVS nomenclature the description p.(Phe2_Leu3delinsPheVal) is not
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Notation for multi-amino-acid silent mutations
Dear Steve, indeed, following HGVS nomenclature the description p.(Phe2_Leu3delinsPheVal) is not
Feb 26
Steven Roels
,
Johan den Dunnen
3
Feb 26
notation for frameshift variants with preceding missense
Dear Steve, without giving a reference sequence, it is difficult to be sure the answer given is
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notation for frameshift variants with preceding missense
Dear Steve, without giving a reference sequence, it is difficult to be sure the answer given is
Feb 26
alessandra tessa
,
J.F.J...@lumc.nl
3
Feb 5
help to define correct nomenclature in complex genomic rearrangement
Thank you very much for your feedback. Alessandra Il giorno lun 5 feb 2024 alle ore 09:24 <JFJ
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help to define correct nomenclature in complex genomic rearrangement
Thank you very much for your feedback. Alessandra Il giorno lun 5 feb 2024 alle ore 09:24 <JFJ
Feb 5
Elspeth Bruford
,
Johan den Dunnen
2
Feb 2
general HGVS queries?
Dear Elspeth, yes, questions about HGVS nomenclature can be asked here or by mailing to the old
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general HGVS queries?
Dear Elspeth, yes, questions about HGVS nomenclature can be asked here or by mailing to the old
Feb 2
Lavanya G
, …
Marina DiStefano
5
Jan 31
Nomenclature Query
Dear Lakshmi, Thanks for the query. I'm not sure if you joined the HGVS google group, so
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Nomenclature Query
Dear Lakshmi, Thanks for the query. I'm not sure if you joined the HGVS google group, so
Jan 31
COOVADIA, ADAM
, …
Ivo Fokkema
3
Jan 26
Describing a delinsinv
Dear all, Actually, because NM_032446.3:c.[2894_2907del;2908_2967inv;2968_3026-7del] contains an
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Describing a delinsinv
Dear all, Actually, because NM_032446.3:c.[2894_2907del;2908_2967inv;2968_3026-7del] contains an
Jan 26
João Gonçalves
,
Johan den Dunnen
2
Jan 26
Nomenclature - Gene duplications
Dear João, answering your question, I will start simple, the duplication. Following HGVS nomenclature
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Nomenclature - Gene duplications
Dear João, answering your question, I will start simple, the duplication. Following HGVS nomenclature
Jan 26
Reece Hart
,
Ros Hastings
2
Jan 15
HGVS Nomenclature 21.0.0 now available at hgvs-nomenclature.org
gret news Kind regards Ros Ros Hastings GenQA Consultant ISCN Standing Committee Chair Oxford
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HGVS Nomenclature 21.0.0 now available at hgvs-nomenclature.org
gret news Kind regards Ros Ros Hastings GenQA Consultant ISCN Standing Committee Chair Oxford
Jan 15
Roster, Estella
,
Johan den Dunnen
2
Jan 13
STRC p.Leu1640Phe HGVS nomenclature
Dear Estella, indeed, following HGVS recommendations, the variant should be described as NC_000015.10
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STRC p.Leu1640Phe HGVS nomenclature
Dear Estella, indeed, following HGVS recommendations, the variant should be described as NC_000015.10
Jan 13
Rachel Challis | GENinCode
, …
Clinical Scientist UK | GENinCode
6
Jan 12
Nomenclature confirmation
Hi Ivo, Thanks so much. Can't see it in our inbox, must have been filtered and removed by the
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Nomenclature confirmation
Hi Ivo, Thanks so much. Can't see it in our inbox, must have been filtered and removed by the
Jan 12
Anthony Cheong (Sydney LHD)
,
Johan den Dunnen
2
Jan 12
full gene deletion + hemiygous variant
Dear Anthony, for cases like this HGVS nomenclture has the "Allele format" (see https://
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full gene deletion + hemiygous variant
Dear Anthony, for cases like this HGVS nomenclture has the "Allele format" (see https://
Jan 12
Paolo Tarantino
,
Ivo Fokkema
2
Jan 12
BRCA1 deletion exon1 and 2
Dear Paolo, From the documentation on deletions on DNA level: deletions extending beyond the
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BRCA1 deletion exon1 and 2
Dear Paolo, From the documentation on deletions on DNA level: deletions extending beyond the
Jan 12
杨明
,
Johan den Dunnen
2
Jan 9
A proposal for the definitions of alleles variant
Dear Ming Yang, thanks for your suggestion. The problem with your suggestion is that it restricts the
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A proposal for the definitions of alleles variant
Dear Ming Yang, thanks for your suggestion. The problem with your suggestion is that it restricts the
Jan 9
Hajdušková Martina
,
Johan den Dunnen
2
Jan 9
Question: reporting DNA variants at the transcript & protein level
Dear Martina, the format NM_000350.3:c.1363C>A p.(Leu455Met) is correct, the format NM_000350.3:c.
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Question: reporting DNA variants at the transcript & protein level
Dear Martina, the format NM_000350.3:c.1363C>A p.(Leu455Met) is correct, the format NM_000350.3:c.
Jan 9