| ARCHETYPE ID | openEHR-EHR-CLUSTER.genomic_substitution_variant.v1 |
|---|---|
| Concept | Genomic substitution variant |
| Description | A human genetic sequence change where, compared to a genomic reference sequence, one nucleotide is replaced by one other nucleotide. |
| Use | Use 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.genomic_variant_result 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. All definitions and examples in this archetype follow the HGVS nomenclature. |
| Misuse | Not 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.genomic_deletion_insertion_variant archetype for this purpose. |
| Purpose | To record the details about a substitution variant of human DNA, observed in a genomic sequence. |
| 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/ |
| Copyright | © openEHR Foundation |
| Authors | Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2017-02-23 |
| Other Details Language | Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2017-02-23 |
| Other Details (Language Independent) |
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| Keywords | substitution, variation, genetic, genomic, variant, DNA, chromosome, mutation, nucleotide |
| Lifecycle | published |
| UID | ee5651f0-c1bc-45f7-8a67-15b74b6c24cd |
| Language used | en |
| Citeable Identifier | 1246.145.741 |
| Revision Number | 1.0.4 |
| Archetype Concept Comment | For example: changing 'AGTAgAGG' to 'AGTAtAGG'. |
| items | |
| Position substituted | Position substituted: The position of the substituted nucleotide. For example: for a variant where the reference sequence 'AGTAgAGG' is changed to 'AGTAtAGG', the position substituted is 5. |
| Reference nucleotide | Reference nucleotide: The nucleotide at reference position. For example: for a variant where the reference sequence 'AGTAgAGG' is changed to 'AGTAtAGG', the reference nucleotide is 'G'. |
| New nucleotide | New nucleotide: Substituted nucleotide. For example: for a variant where the reference sequence 'AGTAgAGG' is changed to 'AGTAtAGG', the new nucleotide is 'T'. |
| Reference sequence | Reference sequence: The sequence file used as a reference to describe this variant. Include: openEHR-EHR-CLUSTER.reference_ |
| Other contributors | 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 |
| Translators |
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