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Sequence Variant Nomenclature

These pages summarise HGVS-nomenclature: the recommendations for the description of sequence variants. HGVS-nomenclature is used to report and exchange information regarding variants found in DNA, RNA and protein sequences and serves as an international standard in DNA diagnostics. HGVS-nomenclature is authorised by the Human Genome Variation Society (HGVS), the Human Variome Project (HVP) and the HUman Genome Organization (HUGO).

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Sequence Variant Nomenclature | varnomen.hgvs.org Reviews
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These pages summarise HGVS-nomenclature: the recommendations for the description of sequence variants. HGVS-nomenclature is used to report and exchange information regarding variants found in DNA, RNA and protein sequences and serves as an international standard in DNA diagnostics. HGVS-nomenclature is authorised by the Human Genome Variation Society (HGVS), the Human Variome Project (HVP) and the HUman Genome Organization (HUGO).
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1 sequence variant nomenclature
2 recommendations
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7 open issues
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Sequence Variant Nomenclature | varnomen.hgvs.org Reviews

https://varnomen.hgvs.org

These pages summarise HGVS-nomenclature: the recommendations for the description of sequence variants. HGVS-nomenclature is used to report and exchange information regarding variants found in DNA, RNA and protein sequences and serves as an international standard in DNA diagnostics. HGVS-nomenclature is authorised by the Human Genome Variation Society (HGVS), the Human Variome Project (HVP) and the HUman Genome Organization (HUGO).

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varnomen.hgvs.org varnomen.hgvs.org
1

Sequence Variant Nomenclature

http://varnomen.hgvs.org/history

Search HGVS and VarNomen Facebook. Publications on the description of sequence variants. Below an overview of publications on the subject of sequence variant descriptions, from old to recent. Beaudet AL, Tsui LC (1993). A suggested nomenclature for designating mutations. Hum. Mutat. 2:245-248. Beutler E (1993). The designation of mutations. Am. J. Hum. Genet. 53:783-785. Antonarakis SE, McKusick VA (1994). Discussion on mutation nomenclature. Hum. Mutat. 4:166. Hum Genet. 109:121-124. Den Dunnen JT, Paal...

2

Sequence Variant Nomenclature

http://varnomen.hgvs.org/bg-material/refseq

Search HGVS and VarNomen Facebook. A sequence file that is used as a reference to describe variants. That are present in a sequence analysed. Only public files from NCBI or EBI are accepted as a reference sequence. Approved reference sequence formats include; NC # (e.g. NC 000023.10), LRG # (e.g. LRG 199), NG # (e.g. NG 012232.1), NM # (e.g. NM 004006.2), NR # (e.g. NR 002196.1) and NP # (e.g. NP 003997.1). A reference sequence file identifier should contain both the accession. NG 012232 .1. Is a genomic...

3

Sequence Variant Nomenclature

http://varnomen.hgvs.org/versioning

Search HGVS and VarNomen Facebook. The current HGVS version number is shown in the top right corner of this web site (. Note that the version does not change when a typing error is corrected, an example added, an explanation clarified, a question answered, etc. The current version is HGVS nomenclature v15.11. Is described in Den Dunnen et al. (2016) HGVS recommendations for the description of sequence variants: 2016 update. Hum.Mutat. 25: 37: 564-569. Allows descriptions like NR 028379.1:n.345A G. As the...

4

Sequence Variant Nomenclature

http://varnomen.hgvs.org/recommendations/general

Search HGVS and VarNomen Facebook. Since references to web sites are not yet acknowledged as citations, please mention Den Dunnen et al. (2016) HGVS recommendations for the description of sequence variants: 2016 update. Hum.Mutat. 25: 37: 564-569. When referring to these pages. Note that although the examples on these pages mainly give examples for human (. The recommendations can be applied to all species. All variants should be described at the most basic level, the DNA level. For an RNA reference sequ...

5

Sequence Variant Nomenclature

http://varnomen.hgvs.org/recommendations/checklist

Search HGVS and VarNomen Facebook. Going through publications one can easily see where people give variant descriptions that do not correctly follow HGVS nomenclature. The checklist below covers the most frequently offended rules. Going through should assist you while preparing a publication containing sequence variant descriptions. Do you clearly mention the reference sequence used for numbering (nucleotides/amino acids)? Do you mention a. Bank) RefSeq-file with accession. And non-coding DNA ( n. Do you...

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cancer.sanger.ac.uk cancer.sanger.ac.uk

COSMIC: Data Submission Page

http://cancer.sanger.ac.uk/cosmic/submissions

I am an author, how should I describe mutation data in my publications? We list here some guidelines for authors to help improve the speed of curation for an increasing volume of literature relevant to COSMIC and to ensure the continuing accuracy of our curation. By following these guidelines authors will contribute to the quick and efficient dissemination of their research results via COSMIC. It is much easier and quicker for us to map reported mutations to COSMIC reference sequences if the author has s...

factorix.org factorix.org

Factor IX Variant Database

http://www.factorix.org/sequence.html.php

Clicking and Dragging the mouse over the sequences will take you across the sequence limits. All numbering is for human FIX and is HGVS. Multiple Sequence Alignment of putative FIX protein sequence from selected species. Multiple Sequence Alignment of Human Vitamin K dependent coagulation factors serine protease domains. Gower Street, London WC1E 6BT.

grch37-cancer.sanger.ac.uk grch37-cancer.sanger.ac.uk

COSMIC: Data Submission Page

http://grch37-cancer.sanger.ac.uk/cosmic/submissions

I am an author, how should I describe mutation data in my publications? We list here some guidelines for authors to help improve the speed of curation for an increasing volume of literature relevant to COSMIC and to ensure the continuing accuracy of our curation. By following these guidelines authors will contribute to the quick and efficient dissemination of their research results via COSMIC. It is much easier and quicker for us to map reported mutations to COSMIC reference sequences if the author has s...

mutalyzer.nl mutalyzer.nl

Mutalyzer 2.0.21 — Name Checker

https://www.mutalyzer.nl/name-checker

HGVS Sequence Variant Nomenclature. Please insert a variant description using the HGVS. AB026906.1:c.40 42del. NG 012337.1(SDHD v001):c.274G T. Mutalyzer 2.0.21. Released on 24 Jun 2016. HGVS nomenclature version 2.0.

cf.eqascheme.org cf.eqascheme.org

CF Network - Nomenclature

http://cf.eqascheme.org/info/public/education/nomenclature.xhtml

Mutation nomenclature in practice: Findings and recommendations from the cystic fibrosis external quality assessment scheme. Berwouts S, Morris MA, Girodon E, Schwarz M, Manfred S, Dequeker E. Human Mutation, 2011, 32 (11), 1197-1203. HGVS Nomenclature for the description of sequence variants. HUGO Mutation Database Initiative. Cystic Fibrosis Mutation Database. Standard mutation nomenclature in molecular diagnostics - Practical and educational challenges. Journal of Molecular Diagnostics, 2007, 9:1-6.

mutalyzer.nl mutalyzer.nl

Mutalyzer 2.0.21 — Syntax Checker

https://www.mutalyzer.nl/syntax-checker

HGVS Sequence Variant Nomenclature. Please insert a variant description using the HGVS. AB026906.1:c.40 42del. NG 012337.1(SDHD v001):c.274G T. Mutalyzer 2.0.21. Released on 24 Jun 2016. HGVS nomenclature version 2.0.

eahad-db.org eahad-db.org

EAHAD VARIANT DATABASES

http://www.eahad-db.org/citations.html.php

If you find our databases useful, please reference our publications:. Factor IX Mutation Database:. Rallapalli, pm, Kemball-Cook, G., Tuddenham, E.G., Gomez, K., and Perkins, S.J. 2013. An interactive mutation database for human coagulation factor IX provides novel insights into the phenotypes and genetics of haemophilia B. 11(7):1329-1340 available from: PM:23617593. VWF Online Database (VWFdb). 37(5):470-479 available from: PM:22102189. 2010 , EAHAD.

eahad-db.org eahad-db.org

EAHAD VARIANT DATABASES

http://www.eahad-db.org/people.html.php

Organisation of the EAHAD Variant Databases Project. The EAHAD Coagulation Factors Variant Database Project is administered by the following groups:. EAHAD Variant Database Steering Group. EAHAD Variant Database Curator Group. EAHAD Individual Variant DB Advisory Committees. 2010 , EAHAD. No part of this site may be copied or used in any way without permission.

eahad-db.org eahad-db.org

EAHAD VARIANT DATABASES

http://www.eahad-db.org/db-policy.html.php

The European Association for Haemophilia and Allied Disorders (EAHAD) Coagulation Factor Mutation Databases. Are maintained and provided as a public service for the clinical, diagnostic and coagulation factor research communities. Beyond limited editorial control and some integrity checks, the quality and accuracy of the record is the responsibility of the submitter, not of the database. The database curators will work with submitters and users of the database to achieve the best quality resource pos...

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varnomen.hgvs.org varnomen.hgvs.org

Sequence Variant Nomenclature

Search HGVS and VarNomen Facebook. What is the sequence variant nomenclature? An overview of recent additions, especially those that led to a change of the. Can be found on the. Page shows whether there are proposals open for. And which topics are currently. VarNomen @ HGVS.org. Follow us on Facebook. Human Genome Variation Society. Discussions regarding HGVS nomenclature are necessary in order to further improve them. What is listed on these pages represents the current consensus of the recommendati...

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