ARCHETYPE Genomic substitution variant (openEHR-EHR-CLUSTER.genomic_substitution_variant.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.genomic_substitution_variant.v0
ConceptGenomic substitution variant
DescriptionA human genetic sequence change where, compared to a genomic reference sequence, one nucleotide is replaced by one other nucleotide.
UseUse to record the details about a substitution variant of human DNA, observed in a genomic sequence. This archetype has been specifically designed to be used in the 'Structured variant' SLOT within the CLUSTER.genetic_variant archetype, but can also be used within other ENTRY or CLUSTER archetypes, where clinically appropriate. In the examples in this archetype, lower case nucleotides are only intended to highlight the changed positions of the DNA sequence.
MisuseNot to be used to record information about variants of non-human DNA, or any kind of RNA or protein. Not to be used to record a change involving two or more consecutive nucleotides. Use the CLUSTER.indel_variant archetype for this purpose.
PurposeTo record the details about a substitution variant of human DNA, observed in a genomic sequence.
Referencesden Dunnen JT, Dalgleish R, Maglott DR, Hart RK, Greenblatt MS, McGowan-Jordan J, Roux AF, Smith T, Antonarakis SE, Taschner PE. HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Hum Mutat. 2016 Jun;37(6):564-9. doi: 10.1002/humu.22981. Epub 2016 Mar 25. PubMed PMID: 26931183.

Sequence Variant Nomenclature - DNA Recommendations - Substitution Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/substitution/
Copyright© openEHR Foundation
AuthorsAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2017-02-23
Other Details LanguageAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2017-02-23
OtherDetails Language Independent{licence=This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/., custodian_organisation=openEHR Foundation, references=den Dunnen JT, Dalgleish R, Maglott DR, Hart RK, Greenblatt MS, McGowan-Jordan J, Roux AF, Smith T, Antonarakis SE, Taschner PE. HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Hum Mutat. 2016 Jun;37(6):564-9. doi: 10.1002/humu.22981. Epub 2016 Mar 25. PubMed PMID: 26931183. Sequence Variant Nomenclature - DNA Recommendations - Substitution Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/substitution/, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=8ECE95D0FBE6967B66202F6DB00A69C9, build_uid=3fa783b8-2467-4a30-b54a-e6581265eac8, revision=0.0.1-alpha}
Keywordssubstitution, variation, genetic, genomic, variant
Lifecyclein_development
UIDb91ee240-6fdc-4b02-a8a4-317830fe904d
Language useden
Citeable Identifier1246.145.741
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A human genetic sequence change where, compared to a genomic reference sequence, one nucleotide is replaced by one other nucleotide., archetypeConceptComment=For example: changing 'AGTAgAGG' to 'AGTAtAGG'., otherContributors=Christina Jaeger-Schmidt, Heidelberg University Hospital, Germany
Florian Kaercher, Charité Berlin, Germany
Francesca Frexia, CRS4, Italy
Gianluigi Zanetti, CRS4, Italy
Heather Leslie, Atomica Informatics, Australia (openEHR Editor)
Gideon Giacomelli, Charité Berlin, Germany
Paolo Uva, CRS4, Italy
Silje Ljosland Bakke, Nasjonal IKT HF, Norway (openEHR Editor)
Simon Schumacher, HiGHmed, Germany
Gunnar Houge, Haukeland University Hospital, Norway
Gyri Aasland Gradek, Haukeland University Hospital, Norway
Asbjørg Stray-Pedersen, Oslo University Hospital, Norway
Toril Fagerheim, University Hospital of North Norway, Norway
Camilla F. Skjelbred, Telemark HF Hospital, Norway
Dag Erik Undlien, Oslo University Hospital, Norway
Rune Østern, St Olavs Hospital, Norway, originalLanguage=en, translators=German: Aurelie Tomczak, Institute of Pathology, University Hospital Heidelberg, Germany, au.tomczak@yahoo.com
Norwegian Bokmål: Liv Laugen, Oslo University Hospital, Norway, liv.laugen@ous-hf.no
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