81251-1
Complex genetic variant panel
Trial
81260-2 Complex genetic variant [ID]
Term Description
This term is used to report the unique identifier of the complex variant found in this study. The identifier may come from various sources, including NCBI's ClinVar and Ensembl. For example, the variant NM_000106.5(CYP2D6):c.[886C>T;457G>C] - Haplotype has the ClinVar ID 16895. http://www.ncbi.nlm.nih.gov/clinvar/variation/16895/
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Complex variant
- Property
- ID
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.58 (MIN)
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Komplexní varianta: |
| el-GR | Greek (Greece) | Σύνθετη παραλλαγή: Synonyms: - MOLPATH Nom Pt Αναγνωριστικό Ασθενής Σύνθετη παραλλαγή |
| es-ES | Spanish (Spain) | Variante compleja: |
| es-MX | Spanish (Mexico) | Variante compleja: |
| fr-FR | French (France) | Variant complexe: |
| it-IT | Italian (Italy) | Variante complessa: Synonyms: Identificatore Patologia molecolare paziente Punto nel tempo (episodio) |
| zh-CN | Chinese (China) | 复杂变异: Synonyms: 分子病理学; |
81262-8 Complex variant HGVS name
Term Description
This term is used to report the name of the complex variant found in this study in HGVS format. For example, c.[886C>T;457G>C], which represents two separate base substitutions in one gene on one chromosome, or c.[886C>T];[457G>C], which represents two separate base substitutions in one gene on two different chromosomes.
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Complex variant HGVS name
- Property
- Find
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.56 (ADD)
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Komplexní varianta HGVS název: |
| el-GR | Greek (Greece) | Όνομα HGVS σύνθετης παραλλαγής: Synonyms: - MOLPATH Nom Pt Ασθενής Εύρεση Όνομα Όνομα HGVS σύνθετης παραλλαγής Σύνθετη παραλλαγή |
| es-ES | Spanish (Spain) | Nombre de la variante compleja HGVS: |
| es-MX | Spanish (Mexico) | Nombre de la variante compleja de HGVS: |
| fr-FR | French (France) | Variant complexe HGVS nom: |
| it-IT | Italian (Italy) | Variante complessa nome HGVS: Synonyms: Osservazione Patologia molecolare paziente Punto nel tempo (episodio) |
| zh-CN | Chinese (China) | 复杂变异 HGVS 命名: Synonyms: 分子病理学; |
81263-6 Complex variant type
Term Description
The type of complex variant, for example, compound heterozygous or haplotype.
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Complex variant type
- Property
- Type
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.56 (ADD)
- Order vs. Observation
- Observation
Example Answer List LL3999-1
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Compound heterozygous | LA26217-2 | ||
| Double heterozygous | LA26220-6 | ||
| Haplotype | LA26218-0 | ||
| Hemizygous | LA6707-9 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Komplexní varianta typ: |
| el-GR | Greek (Greece) | Τύπος σύνθετης παραλλαγής: Synonyms: - MOLPATH Nom Pt Type Ασθενής Σύνθετη παραλλαγή Τύπος σύνθετης παραλλαγής |
| es-ES | Spanish (Spain) | Tipo de variante compleja: |
| es-MX | Spanish (Mexico) | Tipo de variante compleja: |
| fr-FR | French (France) | Variant complexe type: |
| it-IT | Italian (Italy) | Tipo di variante complessa: Synonyms: Patologia molecolare paziente Punto nel tempo (episodio) |
| zh-CN | Chinese (China) | 复杂变异类型: Synonyms: 分子病理学; |
81259-4 Associated phenotype
Term Description
The possible phenotype associated with the genetic variant found in this study.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Associated phenotype
- Property
- Find
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.71 (MIN)
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Asociovaný fenotyp: |
| el-GR | Greek (Greece) | Συνδεδεμένος φαινότυπος: Synonyms: - MOLPATH Nom Pt Ασθενής Εύρεση Συνδεδεμένος φαινότυπος |
| es-ES | Spanish (Spain) | Fenotipo asociado probable: |
| es-MX | Spanish (Mexico) | Fenotipo asociado: |
| fr-FR | French (France) | Phénotype associé: |
| it-IT | Italian (Italy) | Probabile fenotipo associato: Synonyms: Osservazione Patologia molecolare paziente Punto nel tempo (episodio) |
| pl-PL | Polish (Poland) | Powiązany fenotyp: Synonyms: Fenotyp towarzyszący wynik kategorialny |
| zh-CN | Chinese (China) | 关联表型: Synonyms: 关联（相关、 |
53037-8 Genetic variation clinical significance [Imp]
Term Description
Single DNA marker or individual allele interpretation in the context of the assessed genetic disease.
Prior to the LOINC release 2.56 (June 2016), the answer list was updated per the recommendations of the American College of Medical Genetics (ACMG). The previous answer list number was LL603-2, and two of the answer strings and LA codes are the same in the new list (pathogenic and benign). In the new answer list, the presumed pathogenic, unknown significance and presumed benign answers from LL603-2 have been replaced by likely pathogenic, uncertain significance and likely benign. The answer strings and their respective LA codes from LL603-2 remain valid.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Genetic disease sequence variation interpretation
- Property
- Imp
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.24
- Last Updated
- Version 2.73 (MIN)
- Change Reason
- Updated LCN per CJM for HL7 CG IG
- Order vs. Observation
- Observation
- Common Test Rank Get Info
- 11949
Preferred Answer List LL4034-6
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Pathogenic | LA6668-3 | ||
| Likely pathogenic | LA26332-9 | ||
| Uncertain significance | LA26333-7 | ||
| Likely benign | LA26334-5 | ||
| Benign | LA6675-8 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 51975-1 | Individual allele results panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Genetické onemocnění sekvenční varianta identifikátor: |
| el-GR | Greek (Greece) | Ερμηνεία παραλλαγών αλληλουχίας γενετικών ασθενειών: Synonyms: HL7.GENETICS Imp Nom Pt Αίμα Αίμα/Ιστός Ερμηνεία Ερμηνεία παραλλαγών αλληλουχίας γενετικών ασθενειών Ιστός Μοριακή γενετική |
| es-ES | Spanish (Spain) | Interpretación de la variante de secuencia de la enfermedad genética: |
| es-MX | Spanish (Mexico) | Interpretación de la variación de la secuencia de la enfermedad genética: |
| fr-FR | French (France) | Maladie génétique interprétation globale de la variation de séquence: |
| it-IT | Italian (Italy) | Malattia genetica, interpretazione variazione di sequenza: Synonyms: Genetica molecolare Impressione/interpretazione di studio Interpretazione della variazione di sequenza di ma Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | genetische ziekte sequentievariatie interpretatie: Synonyms: molgen |
| pl-PL | Polish (Poland) | Interpretacja wariantów sekwencyjnych chorób genetycznych: Synonyms: diagnostyka molekularna Interpretacja wariantów sekwencyjnych w chorobach genetycznych wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Doença genética interpretação variação da seqüência: Synonyms: Interp; |
| ru-RU | Russian (Russian Federation) | Генетическое заболевание последовательность вариация интерпретация: Synonyms: Впечатление/интерпретация исследования Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Genetik hastalık sekans varyasyon yorumu: |
| zh-CN | Chinese (China) | 遗传性疾病序列变异解释: Synonyms: HL7 遗传学 全血或组织; |
53034-5 Allelic state
Term Description
The level of occurrence of a single DNA Marker within a set of chromosomes. Heterozygous indicates the DNA Marker is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Marker is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Marker exists in the only single copy of a gene in a non-homologous chromosome (The male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Marker is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Maker is present in all of the copies of mitochondrial DNA.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Allelic state
- Property
- Find
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.24
- Last Updated
- Version 2.68 (MIN)
- Order vs. Observation
- Observation
Preferred Answer List LL381-5
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Heteroplasmic | LA6703-8 | ||
| Homoplasmic | LA6704-6 | ||
| Homozygous | LA6705-3 | ||
| Heterozygous | LA6706-1 | ||
| Hemizygous | LA6707-9 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Alelický stav: |
| el-GR | Greek (Greece) | Κατάσταση αλληλομόρφων: Synonyms: HL7.GENETICS Nom Pt Αίμα Αίμα/Ιστός Εύρεση Ιστός Κατάσταση Κατάσταση αλληλομόρφων Μοριακή γενετική |
| es-ES | Spanish (Spain) | Estado alélico: |
| es-MX | Spanish (Mexico) | Estado alélico: |
| fr-FR | French (France) | Statut allélique: |
| it-IT | Italian (Italy) | Stato allelico: Synonyms: Genetica molecolare Osservazione Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | allelstatus: Synonyms: molgen |
| pl-PL | Polish (Poland) | Status alleliczny: Synonyms: diagnostyka molekularna wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Estado alélicas: Synonyms: Finding; |
| ru-RU | Russian (Russian Federation) | Аллельное состояние: Synonyms: Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Allelik durum: |
| zh-CN | Chinese (China) | 等位状态: Synonyms: HL7 遗传学 全血或组织; |
82309-6 Basis for allelic phase [Type]
Part Descriptions
LP220487-5 Basis for allelic phase
The evidential basis on which the allelic phase and/or the allelic state was concluded.
Choices include:
1) Directly measured;
2) Family DNA;
3) Family history;
4) Inferred from population data
Source: Regenstrief LOINC
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Basis for allelic phase
- Property
- Type
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
- *
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.58
- Last Updated
- Version 2.58 (ADD)
- Order vs. Observation
- Observation
Example Answer List LL4050-2
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Directly measured | LA26426-9 | ||
| Family DNA | LA26427-7 | ||
| Family history | LA26428-5 | ||
| Inferred from population data | LA26429-3 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Základ pro alelickou fázi: |
| el-GR | Greek (Greece) | Βάση για φάση αλληλόμορφων: Synonyms: - * MOLPATH Nom Pt Type Ασθενής Βάση για φάση αλληλόμορφων Φάση αλληλομόρφων |
| es-ES | Spanish (Spain) | Bases para la fase alélica: |
| es-MX | Spanish (Mexico) | Base para la fase alélica: |
| fr-FR | French (France) | Bases de la phase allélique: |
| it-IT | Italian (Italy) | Fondamenti di fase allelica: Synonyms: Patologia molecolare paziente Punto nel tempo (episodio) |
| nl-NL | Dutch (Netherlands) | basis voor allelische fase: |
| pl-PL | Polish (Poland) | Podstawy na bazie której oceniany jest układ alleli: Synonyms: Konfiguracja alleli wynik kategorialny |
| zh-CN | Chinese (China) | 等位基因相的依据: Synonyms: 分子病理学; |
81250-3 Discrete genetic variant panel
Term Description
This panel is used to report the information associated with a simple genetic variant, such as a single nucleotide change. It should not be used to report information related to structural variants.
Fully-Specified Name
- Component
- Simple variant panel
- Property
- -
- Time
- Pt
- System
- ^Patient
- Scale
- -
- Method
Basic Attributes
- Class
- PANEL.MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.58 (MIN)
- Order vs. Observation
- Order
- Panel Type
- Panel
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Varianta jednoduchá panel: |
| el-GR | Greek (Greece) | Πίνακας απλών παραλλαγών: Synonyms: - MOLPATH PANEL.MOLPATH Pt Απλή παραλλαγή Ασθενής Πίνακας απλών παραλλαγών |
| es-ES | Spanish (Spain) | Panel de variante simple: |
| es-MX | Spanish (Mexico) | Panel de variante simple: |
| fr-FR | French (France) | Variant simple panel: |
| it-IT | Italian (Italy) | Variante semplice panel: Synonyms: Panel variante semplice Patologia molecolare paziente Punto nel tempo (episodio) Set di prescrizione patologia molecolare |
| zh-CN | Chinese (China) | 简单变异组套: Synonyms: 分子病理学; |
83005-9 Variant category
Fully-Specified Name
- Component
- Variant category
- Property
- Type
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.58
- Last Updated
- Version 2.58 (ADD)
- Order vs. Observation
- Observation
Example Answer List LL4165-8
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Simple variant | LA26801-3 | ||
| Structural variant | LA26802-1 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Varianta kategorie: |
| el-GR | Greek (Greece) | Κατηγορία παραλλαγής: Synonyms: - MOLPATH Nom Pt Type Ασθενής Κατηγορία παραλλαγής |
| es-ES | Spanish (Spain) | Categoría variante: |
| es-MX | Spanish (Mexico) | Categoría de variante: |
| fr-FR | French (France) | Catégorie de variant: |
| it-IT | Italian (Italy) | Categoria variante: Synonyms: Patologia molecolare paziente Punto nel tempo (episodio) |
| zh-CN | Chinese (China) | 变异类别: Synonyms: 分子病理学; |
81252-9 Discrete genetic variant
Term Description
This term is used to report the unique identifier of the simple variant found in this study. The identifier may come from various sources, including NCBI's ClinVar and Ensembl. For example, the variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys) has the ClinVar ID 30880 and would be reported in OBX-5 as 30880^NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)^ClinVar. http://www.ncbi.nlm.nih.gov/clinvar/variation/30880/
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Simple variant
- Property
- ID
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.58 (MIN)
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Jednoduchá varianta: |
| el-GR | Greek (Greece) | Απλή παραλλαγή: Synonyms: - MOLPATH Nom Pt Αναγνωριστικό Απλή παραλλαγή Ασθενής |
| es-ES | Spanish (Spain) | Variante simple: |
| es-MX | Spanish (Mexico) | Variante simple: |
| fr-FR | French (France) | Variant simple: |
| it-IT | Italian (Italy) | Variante semplice: Synonyms: Identificatore Patologia molecolare paziente Punto nel tempo (episodio) |
| zh-CN | Chinese (China) | 简单变异: Synonyms: 分子病理学; |
48018-6 Gene studied [ID]
Term Description
HUGO Gene Nomenclature Committee (HGNC) identifier for a gene. List the gene(s) examined in full or in part by the study. If the study addresses multiple genes, these can be recorded in one OBX as a list seperated by repeat delimiters or in mulltiple OBX's with one gene per OBX. The recommended coding system will use the HGNC gene symbol as the display text and HGNC gene ID as the code. For example, 21497^ACAD9^HGNC.
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Gene identifier
- Property
- ID
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.21
- Last Updated
- Version 2.73 (MIN)
- Order vs. Observation
- Observation
- Common Test Rank Get Info
- 9796
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 77313-5 | DNA analysis discrete sequence variation basic associated observations panel - Blood or Tissue by Molecular genetics method |
| 53042-8 | DNA marker assessed panel |
| 53044-4 | DNA marker identified panel |
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 111577-3 | Hematologic malignancy gene fusion panel - Specimen by Molecular genetics method |
| 48015-2 | Individual allele panel |
| 51975-1 | Individual allele results panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
| 78046-0 | Pharmacogenomic analysis basic associated observations panel - Blood or Tissue |
| 102118-7 | Rhabdomyolysis and Metabolic myopathy multigene panel - Blood or Tissue by Molecular genetics method |
| 48014-5 | Sequence variation panel - Blood or Tissue by Molecular genetics method |
| 48017-8 | Sequencing methodology panel - Blood or Tissue by Molecular genetics method |
| 102119-5 | Skeletal muscle channelopathy multigene panel - Blood or Tissue by Molecular genetics method |
| 74028-2 | Virtual Medical Record for Clinical Decision Support panel HL7.VMR-CDS |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Gen zkoumaný identifikátor: |
| el-GR | Greek (Greece) | Αναγνωριστικό γονιδίου: Synonyms: HL7.GENETICS Nom Pt Αίμα Αίμα/Ιστός Αναγνωριστικό Αναγνωριστικό γονιδίου Γονίδιο Ιστός |
| es-ES | Spanish (Spain) | Identificador genético: |
| es-MX | Spanish (Mexico) | Identificador de gen estudiado: |
| fr-FR | French (France) | Gène identifiant: |
| it-IT | Italian (Italy) | Gene, identificatore: Synonyms: Identificatore Identificatore del gene Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | gen-identificator: |
| pl-PL | Polish (Poland) | Identyfikator genu: Synonyms: wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Identificação do gene: Synonyms: ; |
| ru-RU | Russian (Russian Federation) | Ген идентификатор: Synonyms: Идентификатор Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Gen tanımlayıcı: |
| zh-CN | Chinese (China) | 基因标识符: Synonyms: HL7 遗传学 全血或组织; |
51958-7 Transcript reference sequence [ID]
Term Description
This field carries the ID for the transcribed reference sequence, which is the part of the genomic reference sequence that is converted to messenger RNA (i.e., after the introns are removed). The transcript reference sequence ID may be reporting using various coding systems including NCBI's RefSeq ("NM_..."), Ensembl ("ENST..."), and LRG ("LRG..." plus "t1" to indicate transcript).
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Transcript reference sequence identifier
- Property
- ID
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.24
- Last Updated
- Version 2.73 (MIN)
- Order vs. Observation
- Observation
- Common Test Rank Get Info
- 14335
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 77313-5 | DNA analysis discrete sequence variation basic associated observations panel - Blood or Tissue by Molecular genetics method |
| 53042-8 | DNA marker assessed panel |
| 53044-4 | DNA marker identified panel |
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 48015-2 | Individual allele panel |
| 51975-1 | Individual allele results panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
| 78046-0 | Pharmacogenomic analysis basic associated observations panel - Blood or Tissue |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Transkripce referenční sekvence identifikátor: |
| el-GR | Greek (Greece) | Αναγνωριστικό αλληλουχίας αναφοράς μεταγραφής: Synonyms: HL7.GENETICS Nom Pt Αίμα Αίμα/Ιστός Ακολουθία αναφοράς Αναγνωριστικό Αναγνωριστικό αλληλουχίας αναφοράς μεταγραφής Ιστός |
| es-ES | Spanish (Spain) | Identificador de secuencia de referencia transcrita: |
| es-MX | Spanish (Mexico) | Identificador de secuencia de referencia de la transcripción: |
| fr-FR | French (France) | Séquence de référence du transcript identifiant: |
| it-IT | Italian (Italy) | Trascrizione, identificatore sequenza di riferimento: Synonyms: Identificatore Identificatore di sequenza di riferimento di trasc Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | transcriptie referentiesequentie identificator: |
| pt-BR | Portuguese (Brazil) | Transcrição identificador seqüência de referência: Synonyms: ; |
| ru-RU | Russian (Russian Federation) | Транскрипт референсная последовательность идентификатор: Synonyms: Идентификатор Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Transkript referans sekans tanımlayıcı: |
| zh-CN | Chinese (China) | 转录物参考序列标识符: Synonyms: HL7 遗传学 全血或组织; |
48004-6 DNA change (c.HGVS)
Term Description
Human Genome Variation Society (HGVS) nomenclature for a single DNA marker. The use of the nomenclature must be extended to describe non-variations (aka. wild types) see samples for wild type examples.
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- DNA change
- Property
- Find
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.21
- Last Updated
- Version 2.73 (MIN)
- Change Reason
- Updated LCN per CJM for HL7 CG IG; Changed Component from "DNA sequence variation" to conform with the balloted HL7 v2 IG
- Order vs. Observation
- Observation
- Common Test Rank Get Info
- 8938
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 77313-5 | DNA analysis discrete sequence variation basic associated observations panel - Blood or Tissue by Molecular genetics method |
| 53044-4 | DNA marker identified panel |
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 48015-2 | Individual allele panel |
| 51975-1 | Individual allele results panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
| 48014-5 | Sequence variation panel - Blood or Tissue by Molecular genetics method |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | DNA změna: |
| el-GR | Greek (Greece) | Αλλαγή DNA: Synonyms: DNA HL7.GENETICS Nom Pt Αίμα Αίμα/Ιστός Αλλαγή DNA Εύρεση Ιστός Μοριακή γενετική |
| es-ES | Spanish (Spain) | Cambio del ADN: |
| es-MX | Spanish (Mexico) | Cambio de ADN: |
| fr-FR | French (France) | ADN variation: |
| it-IT | Italian (Italy) | DNA, cambio: Synonyms: Cambio di DNA Genetica molecolare Osservazione Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| pl-PL | Polish (Poland) | Zmiana w DNA: Synonyms: diagnostyka molekularna Kwas deoksyrybonukleinowy wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Variação da sequência de DNA: Synonyms: ; |
| zh-CN | Chinese (China) | DNA 变化: Synonyms: DNA 改变 HL7 遗传学 全血或组织; |
48005-3 Amino acid change (pHGVS)
Term Description
Human Genome Variation Society (HGVS) nomenclature for an amino acid sequence. This value is derivable from the DNA Marker value if available. It is provided for convenience. The use of the nomenclature must be extended to describe non-variations (aka. wild types) see samples for wild type examples.
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Amino acid change
- Property
- Find
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.21
- Last Updated
- Version 2.73 (MIN)
- Change Reason
- Updated LCN per CJM for HL7 CG IG
- Order vs. Observation
- Observation
- Common Test Rank Get Info
- 4958
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 53042-8 | DNA marker assessed panel |
| 53044-4 | DNA marker identified panel |
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 48015-2 | Individual allele panel |
| 51975-1 | Individual allele results panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
| 48014-5 | Sequence variation panel - Blood or Tissue by Molecular genetics method |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Aminokyselina změna: |
| el-GR | Greek (Greece) | Αλλαγή αμινοξέων: Synonyms: HL7.GENETICS Nom Pt Αίμα Αίμα/Ιστός Αλλαγή αμινοξέων Εύρεση Ιστός Μοριακή γενετική |
| es-ES | Spanish (Spain) | cambio aminoacídico: |
| es-MX | Spanish (Mexico) | Cambio de aminoácidos: |
| fr-FR | French (France) | Acides aminés substitués: |
| it-IT | Italian (Italy) | Aminoacido, cambio: Synonyms: Cambio di aminoacido Genetica molecolare Osservazione Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | aminozuurwijziging: Synonyms: molgen |
| pl-PL | Polish (Poland) | Zmiana aminokwasu: Synonyms: diagnostyka molekularna wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Mudança de amino ácido: Synonyms: Finding; |
| ru-RU | Russian (Russian Federation) | Аминокислота изменение: Synonyms: Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Amino asit değişimi: |
| zh-CN | Chinese (China) | 氨基酸变化: Synonyms: HL7 遗传学 全血或组织; |
48019-4 DNA change type
Term Description
Codified type for associated DNA Marker. DNA Marker's use the HGVS notation which implies the DNA Marker Type, but the concurrent use of this code will allow a standard and explicit type for technical and display convenience.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- DNA change type
- Property
- Type
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.21
- Last Updated
- Version 2.64 (NAM)
- Change Reason
- Updated LCN per CJM for HL7 CG IG; Changed Component from "DNA sequence variation type" to conform with balloted HL7 v2 IG
- Order vs. Observation
- Observation
Preferred Answer List LL4033-8
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Wild type | LA9658-1 | ||
| Deletion | LA6692-3 | ||
| Duplication | LA6686-5 | ||
| Insertion | LA6687-3 | ||
| Insertion/Deletion | LA6688-1 | ||
| Inversion | LA6689-9 | ||
| Substitution | LA6690-7 | ||
| Copy number gain | LA14033-7 | ||
| Copy number loss | LA14034-5 | ||
| Mobile element insertion | LA26324-6 | ||
| Novel sequence insertion | LA26325-3 | ||
| Tandem duplication | LA26326-1 | ||
| Intrachromosomal breakpoint | LA26327-9 | ||
| Interchromosomal breakpoint | LA26328-7 | ||
| Translocation | LA26331-1 | ||
| Complex | LA26330-3 | ||
| Sequence alteration | LA26329-5 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 53042-8 | DNA marker assessed panel |
| 53044-4 | DNA marker identified panel |
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 48015-2 | Individual allele panel |
| 51975-1 | Individual allele results panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
| 48014-5 | Sequence variation panel - Blood or Tissue by Molecular genetics method |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | DNA změna typ: |
| el-GR | Greek (Greece) | Τύπος αλλαγής DNA: Synonyms: DNA HL7.GENETICS Nom Pt Type Αίμα Αίμα/Ιστός Αλλαγή DNA Ιστός Μοριακή γενετική Τύπος αλλαγής DNA |
| es-ES | Spanish (Spain) | Tipo de cambio del ADN: |
| es-MX | Spanish (Mexico) | Tipo de cambio de ADN: |
| fr-CA | French (Canada) | Type de variation de l'ADN: |
| fr-FR | French (France) | ADN type de variation: |
| it-IT | Italian (Italy) | DNA, cambio tipo: Synonyms: Cambio di DNA Cambio tipo di DNA Genetica molecolare Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| pl-PL | Polish (Poland) | Typ zmiany DNA: Synonyms: diagnostyka molekularna Kwas deoksyrybonukleinowy Rodzaj zmiany w DNA wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Tipo de variação de sequência de DNA: Synonyms: ; |
| zh-CN | Chinese (China) | DNA 变化类型: Synonyms: DNA 改变 DNA 改变类型 HL7 遗传学 全血或组织; |
48006-1 Amino acid change [Type]
Term Description
Codified type for associated Amino Acid Marker. Amino Acid Marker's use the HGVS notation which implies the Amino Acid Marker Type, but the concurrent use of this code will allow a standard and explicit type for technical and display convenience.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Amino acid change type
- Property
- Type
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.21
- Last Updated
- Version 2.58 (MIN)
- Order vs. Observation
- Observation
Preferred Answer List LL380-7
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Wild type | LA9658-1 | ||
| Deletion | LA6692-3 | ||
| Duplication | LA6686-5 | ||
| Frameshift | LA6694-9 | ||
| Initiating Methionine | LA6695-6 | ||
| Insertion | LA6687-3 | ||
| Insertion and Deletion | LA9659-9 | ||
| Missense | LA6698-0 | ||
| Nonsense | LA6699-8 | ||
| Silent | LA6700-4 | ||
| Stop Codon Mutation | LA6701-2 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 53042-8 | DNA marker assessed panel |
| 53044-4 | DNA marker identified panel |
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 48015-2 | Individual allele panel |
| 51975-1 | Individual allele results panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
| 48014-5 | Sequence variation panel - Blood or Tissue by Molecular genetics method |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Aminokyselina změna typ: |
| el-GR | Greek (Greece) | Τύπος αλλαγής αμινοξέων: Synonyms: HL7.GENETICS Nom Pt Type Αίμα Αίμα/Ιστός Αλλαγή αμινοξέων Ιστός Μοριακή γενετική Τύπος αλλαγής αμινοξέων |
| es-ES | Spanish (Spain) | Tipo de cambio aminoacídico: |
| es-MX | Spanish (Mexico) | Tipo de cambio de aminoácidos: |
| fr-FR | French (France) | Acides aminés type de substitution: |
| it-IT | Italian (Italy) | Aminoacido, cambio tipo: Synonyms: Cambio di aminoacido Cambio tipo di aminoacido Genetica molecolare Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | aminozuurwijzigingstype: Synonyms: molgen soort |
| pl-PL | Polish (Poland) | Typ zmiany aminokwasu: Synonyms: diagnostyka molekularna wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Tipo de mudança de amino ácido: Synonyms: Typ; |
| ru-RU | Russian (Russian Federation) | Аминокислота изменение тип: Synonyms: Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Amino asit değişimi tipi: Synonyms: Tür |
| zh-CN | Chinese (China) | 氨基酸变化类型: Synonyms: HL7 遗传学 全血或组织; |
48013-7 Genomic reference sequence [ID]
Term Description
This field carries the ID for the genomic reference sequence. The genomic reference sequence is a contiguous stretch of chromosome DNA that spans all of the exons of the gene and includes transcribed and non transcribed stretches. For this ID use either the NCBI genomic nucleotide RefSeq IDs with their version number (see: NCBI.NLM.NIH.Gov/RefSeq) or use the LRG identifiers, without transcript (t or p) extensions -- when they become available. (See- Report sponsored by GEN2PHEN at the European Bioinformatics Institute at Hinxton UK April 24-25, 2008).
The NCI RefSeq genomic IDs are distinguished by a prefix of"NG" for genes from the nuclear chromosomes and prefix of "NC" for genes from mitochondria. The LRG Identifiers have a prefix of "LRG_" Mitochondrial genes are not in the scope of LRG
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Genomic reference sequence identifier
- Property
- ID
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.21
- Last Updated
- Version 2.58 (MIN)
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 77313-5 | DNA analysis discrete sequence variation basic associated observations panel - Blood or Tissue by Molecular genetics method |
| 53042-8 | DNA marker assessed panel |
| 53044-4 | DNA marker identified panel |
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 48015-2 | Individual allele panel |
| 51975-1 | Individual allele results panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
| 78046-0 | Pharmacogenomic analysis basic associated observations panel - Blood or Tissue |
| 48017-8 | Sequencing methodology panel - Blood or Tissue by Molecular genetics method |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Genomová referenční sekvence identifikátor: |
| el-GR | Greek (Greece) | Αναγνωριστικό αλληλουχίας γονιδιωματικής αναφοράς: Synonyms: HL7.GENETICS Nom Pt Αίμα Αίμα/Ιστός Ακολουθία αναφοράς Αναγνωριστικό Αναγνωριστικό αλληλουχίας γονιδιωματικής αναφοράς Ιστός |
| es-ES | Spanish (Spain) | Identificador de secuencia de referencia genómica: |
| es-MX | Spanish (Mexico) | Identificador de secuencia de referencia genómica: |
| fr-FR | French (France) | Séquence de référence génomique identifiant: |
| it-IT | Italian (Italy) | Sequenza di riferimento genomica, identificatore: Synonyms: Identificatore Identificatore della sequenza genomica di riferime Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | genomische referentie sequentie identificator: |
| pl-PL | Polish (Poland) | Identyfikator referencyjnej sekwencji genomowej: Synonyms: wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Identificador da sequência de referência Genomic: Synonyms: ; |
| ru-RU | Russian (Russian Federation) | Геном референсная последовательность идентификатор: Synonyms: Идентификатор Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Genomik referans sekans tanımlayıcı: |
| zh-CN | Chinese (China) | 基因组参考序列标识符: Synonyms: HL7 遗传学 全血或组织; |
81290-9 Genomic DNA change (gHGVS)
Term Description
The name of a structural variant reported using HGVS nomenclature.
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Genomic DNA change
- Property
- Find
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.58 (NAM)
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Genom DNA změna: |
| el-GR | Greek (Greece) | Αλλαγή γονιδιωματικού DNA: Synonyms: - DNA MOLPATH Nom Pt Αλλαγή DNA Αλλαγή γονιδιωματικού DNA Ασθενής Εύρεση |
| es-ES | Spanish (Spain) | Nombre de la variante estructural HGVS: |
| es-MX | Spanish (Mexico) | Cambio de ADN genómico: |
| fr-FR | French (France) | Variation ADN génomique: |
| it-IT | Italian (Italy) | Variante strutturale nome HGVS: Synonyms: Cambio di DNA Osservazione Patologia molecolare paziente Punto nel tempo (episodio) |
| pl-PL | Polish (Poland) | Zmiana w genomowym DNA: Synonyms: Kwas deoksyrybonukleinowy wynik kategorialny Zmiana w sekwencji genomowego DNA |
| zh-CN | Chinese (China) | 基因组 DNA 变化: Synonyms: DNA 改变 分子病理学; |
69547-8 Genomic ref allele [ID]
Term Description
Reference values ("normal") examined within the Reference Sequence. This is used in a genotyping test to define the reference and variable nucleotide strings. That is if the sequence variation is an insertion, then Reference Nucleotide will be blank and Variable Nucleotide will contain the inserted nucleotides. In contrast, if the sequence variation is a deletion, then the Reference Nucleotide will contain the deleted nucliotieds, and the Variable Nucleotide will be blank.
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Reference nucleotide
- Property
- Prid
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.38
- Last Updated
- Version 2.58 (MIN)
- Change Reason
- Updated LCN per CJM for HL7 CG IG
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 55233-1 | Genetic analysis master panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Referenční nukleotid: |
| el-GR | Greek (Greece) | Νουκλεοτίδιο αναφοράς: Synonyms: HL7.GENETICS Nom Prid Pt Αίμα Αίμα/Ιστός Ιστός Μοριακή γενετική Νουκλεοτίδιο αναφοράς |
| es-ES | Spanish (Spain) | Nucleótido de referencia: |
| es-MX | Spanish (Mexico) | Nucleótido de referencia: |
| fr-FR | French (France) | Nucléotide de référence: |
| it-IT | Italian (Italy) | Nucleotide di riferimento: Synonyms: Genetica molecolare Presenza o Identità Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | referentie nucleotide: Synonyms: molgen |
| pl-PL | Polish (Poland) | Nukleotyd referencyjny: Synonyms: diagnostyka molekularna wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Nucleotídeo de referência: |
| ru-RU | Russian (Russian Federation) | Референс нуклеотид: Synonyms: Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Referans nukleotid: |
| zh-CN | Chinese (China) | 参考核苷酸: Synonyms: HL7 遗传学 全血或组织; |
81254-5 Genomic allele start-end
Term Description
The variant start-end location is the first genomic position in the reference allele that contains a change from the reference allele. For example, for the simple variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys), the variant exact start-end location is Chr3: 128906220 on Assembly GRCh38. http://www.ncbi.nlm.nih.gov/clinvar/variation/30880/
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Variant exact start-end
- Property
- ID
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.68 (NAM)
- Change Reason
- Release 2.68: COMPONENT: Updated to make the reporting of variant location more generalizable (per the HL7 Clinical Genomics Working Group).
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Varianta přesná počáteční a koncová pozice: |
| el-GR | Greek (Greece) | Ακριβές σημείο έναρξης-τέλους παραλλαγής: Synonyms: - MOLPATH Nom Pt Ακριβές σημείο έναρξης-τέλους παραλλαγής Αναγνωριστικό Ασθενής |
| es-ES | Spanish (Spain) | Localización del alelo genómico: |
| es-MX | Spanish (Mexico) | Variante de inicio-fin exacto: |
| fr-FR | French (France) | Variant exact (Début-fin): |
| it-IT | Italian (Italy) | Posizione genomica dell'allele: Synonyms: Identificatore Patologia molecolare paziente Punto nel tempo (episodio) |
| zh-CN | Chinese (China) | 结构变异确切起止位置: Synonyms: 分子病理学; |
69551-0 Genomic alt allele [ID]
Term Description
The genomic alternate allele is the contiguous segment of DNA in the test sample that differs from the reference allele at the same location and thus defines a variant.
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Variable nucleotide
- Property
- Prid
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.38
- Last Updated
- Version 2.58 (MIN)
- Change Reason
- Updated LCN per CJM for HL7 CG IG
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 55233-1 | Genetic analysis master panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Genomová alternativní alela: |
| el-GR | Greek (Greece) | Μεταβλητό νουκλεοτίδιο: Synonyms: HL7.GENETICS Nom Prid Pt Αίμα Αίμα/Ιστός Ιστός Μεταβλητό νουκλεοτίδιο Μοριακή γενετική |
| es-ES | Spanish (Spain) | Nucleótido variable: |
| es-MX | Spanish (Mexico) | Alelo alternativo genómico: |
| fr-FR | French (France) | Nucléotide variable: |
| it-IT | Italian (Italy) | Nucleotide variabile: Synonyms: Genetica molecolare Presenza o Identità Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | variable nucleotide: Synonyms: molgen |
| pt-BR | Portuguese (Brazil) | Nucleotídeo variável: |
| ru-RU | Russian (Russian Federation) | Вариабельный нуклеотид: Synonyms: Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Değişken nükleotid: |
| zh-CN | Chinese (China) | 可变核苷酸: Synonyms: HL7 遗传学 全血或组织; |
84414-2 Haplotype name
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Haplotype name
- Property
- ID
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.58
- Last Updated
- Version 2.58 (ADD)
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Haplotyp název: |
| el-GR | Greek (Greece) | Όνομα απλοτύπου: Synonyms: MOLPATH Nom Pt Αίμα Αίμα/Ιστός Αναγνωριστικό Ιστός Όνομα Όνομα απλοτύπου |
| es-ES | Spanish (Spain) | Nombre Haplotipo: |
| es-MX | Spanish (Mexico) | Nombre del haplotipo: |
| fr-FR | French (France) | Nom haplotype: |
| it-IT | Italian (Italy) | Aplotipo, nome: Synonyms: Identificatore Nome dell''aplotipo Patologia molecolare Punto nel tempo (episodio) Sangue Sangue o Tessuto Tessuto & |
| zh-CN | Chinese (China) | 单体型名称: Synonyms: 全血或组织; |
81255-2 dbSNP [ID]
Term Description
The unique identifier for the variant represented as a small nucleotide polymorphism (SNP). The dbSNP ID is used routinely as the base identifier in pharmacogenomics as well as arrCGH studies. For example, for the simple variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys), the dbSNP ID is 368949613. http://www.ncbi.nlm.nih.gov/clinvar/variation/30880/
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- dbSNP
- Property
- ID
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.58 (MIN)
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Databáze jednonukleotidových polymorfismů dbSNP: |
| el-GR | Greek (Greece) | dbSNP: Synonyms: - dbSNP MOLPATH Nom Pt Αναγνωριστικό Ασθενής |
| es-ES | Spanish (Spain) | dbSNP: |
| es-MX | Spanish (Mexico) | dbSNP: |
| fr-FR | French (France) | dbSNP: |
| it-IT | Italian (Italy) | dbSNP: Synonyms: Identificatore Patologia molecolare paziente Punto nel tempo (episodio) |
| zh-CN | Chinese (China) | dbSNP: Synonyms: 分子病理学; |
81257-8 CIGAR [ID]
Term Description
This term is used to report the unique ID from CIGAR, a syntax for describing variation that is use most frequently during alignment in sequencing studies.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- CIGAR
- Property
- ID
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.58 (MIN)
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | CIGAR: |
| el-GR | Greek (Greece) | CIGAR: Synonyms: - CIGAR MOLPATH Nom Pt Αναγνωριστικό Ασθενής |
| es-ES | Spanish (Spain) | CIGAR: |
| es-MX | Spanish (Mexico) | CIGARRO: |
| fr-FR | French (France) | CIGAR: |
| it-IT | Italian (Italy) | CIGAR: Synonyms: Identificatore Patologia molecolare paziente Punto nel tempo (episodio) |
| pl-PL | Polish (Poland) | CIGAR: Synonyms: CIGAR wynik kategorialny |
| zh-CN | Chinese (China) | CIGAR: Synonyms: 分子病理学; |
48001-2 Cytogenetic (chromosome) location
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Chromosome region
- Property
- ID
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- MOLPATH.MISC
- Type
- Laboratory
- First Released
- Version 2.21
- Last Updated
- Version 2.58 (MIN)
- Change Reason
- Updated LCN per CJM for HL7 CG IG
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
| 48014-5 | Sequence variation panel - Blood or Tissue by Molecular genetics method |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Lokalizace cytogenetická: |
| el-GR | Greek (Greece) | Χρωμοσωμική περιοχή: Synonyms: MISC MOLPATH MOLPATH.MISC Nom Pt Αίμα Αίμα/Ιστός Αναγνωριστικό Ιστός Μοριακή γενετική Περιοχή Χρωμόσωμα Χρωμοσωμική περιοχή |
| es-ES | Spanish (Spain) | Región cromosómica: |
| es-MX | Spanish (Mexico) | Región cromosómica: |
| fr-FR | French (France) | Chromosome région: |
| it-IT | Italian (Italy) | Regione cromosomica: Synonyms: Genetica molecolare Identificatore Miscellanea Miscellanea geni Patologia molecolare Punto nel tempo (episodio) Sangue Sangue o Tessuto Tessuto & |
| ko-KR | Korean (Korea, Republic Of) | 염색체 부위: |
| nl-NL | Dutch (Netherlands) | chromosoomgebied: Synonyms: molgen |
| pl-PL | Polish (Poland) | Region chromosomowy: Synonyms: diagnostyka molekularna wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Região do cromossomo: Synonyms: Chromosomes; |
| ru-RU | Russian (Russian Federation) | Хромосома участок: Synonyms: Идентификатор Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Kromozom bölgesi: |
| zh-CN | Chinese (China) | 染色体区域: Synonyms: 全血或组织; |
48002-0 Genomic source class [Type]
Term Description
The genomic class of the variant: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Genomic source class
- Property
- Type
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.21
- Last Updated
- Version 2.82 (MIN)
- Order vs. Observation
- Observation
- Common Test Rank Get Info
- 14631
Preferred Answer List LL378-1
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Germline | LA6683-2 | ||
| Somatic | LA6684-0 | ||
| Fetal | LA10429-1 | ||
| Likely germline | LA18194-3 | ||
| Likely somatic | LA18195-0 | ||
| Likely fetal | LA18196-8 | ||
| Unknown genomic origin | LA18197-6 | ||
| De novo | LA26807-0 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 62389-2 | Chromosome analysis master panel |
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 51966-0 | Genetic disease DNA analysis panel |
| 51975-1 | Individual allele results panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
| 51962-9 | Pharmacogenetic DNA analysis panel |
| 48014-5 | Sequence variation panel - Blood or Tissue by Molecular genetics method |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Genomový zdroj třída: |
| el-GR | Greek (Greece) | Κατηγορία γονιδιωματικής πηγής: Synonyms: HL7.GENETICS Nom Pt Type Αίμα Αίμα/Ιστός Ιστός Κατηγορία Κατηγορία γονιδιωματικής πηγής Μοριακή γενετική |
| es-ES | Spanish (Spain) | Origen de la clase genómica: |
| es-MX | Spanish (Mexico) | Clase de fuente genómica: |
| fr-FR | French (France) | Source génomique: |
| it-IT | Italian (Italy) | Classe fonte Genomica: Synonyms: Genetica molecolare Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | genomische bronklasse: Synonyms: molgen |
| pl-PL | Polish (Poland) | Klasa zasobów genomowych: Synonyms: diagnostyka molekularna Kategoria zasobów genomicznych wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Classe da fonte Genomic: Synonyms: Genetic variant source; |
| ru-RU | Russian (Russian Federation) | Геномный источник класс: Synonyms: Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Genomik kaynak sınıfı: Synonyms: Tür |
| zh-CN | Chinese (China) | 基因组来源类: Synonyms: HL7 遗传学 全血或组织; |
81304-8 Variant analysis method [Type]
Term Description
The method used for analyzing chromosome structural variation, such as FISH, arrCGH, sequencing, and MLPA.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Structural variant analysis method
- Property
- Type
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
- *
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.58 (MIN)
- Order vs. Observation
- Observation
Example Answer List LL4048-6
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Sequencing Usually refers to high-throughput, next-generation sequencing methods, although can also refer to traditional capillary-based Sanger sequencing. Advantages: a lot of data at little cost. Disadvantages: short read length; high error rates. Next-Gen Sequencing is currently the most popular method for generating genetic data in general, and for detecting both single-nucleotide and structural variation. | LA26398-0 | ||
| Oligo aCGH The use of dense arrays of oligonucleotides deposited on glass slides, subjected to fluorescent Comparative Genomic Hybridization. Probe Intensity Analysis (see Analysis Types below) use test:reference ratios to detect copy number changes. Advantages: one can "scan" an entire genome very rapidly; high sensitivity. Disadvantages: cannot detect inversions or complex rearrangements; cannot determine genomic location of copy number gains (and in some cases losses); resolution not as high as sequencing. Another very popular method for detecting structural variation. | LA26399-8 | ||
| SNP array Originally designed to genotype single nucleotide variation in a massively parallel manner, SNP arrays have many of the same advantages and disadvantages as oligonucleotide arrays. However, they have the added benefit of enabling statistical analysis of allelic inhertance patterns between samples from related individuals, thus adding to their ability to detect and describe de novo structural variation events. | LA26400-4 | ||
| BAC aCGH BAC arrays pre-date oligo arrays and use as probes replicated bacterial artificial chromosome DNA (average insert length ~150 kilobases) and comparative genomic hybridization between a reference and a test sample. Disadvantages: labor-intensive to produce; very low resolution. Not typically in current use. | LA26401-2 | ||
| Curated The manual aggregation and curation of independently reported structural variants from several online resources. These often clinically important variants would not otherwise find their way into a public catalogue of important structural variation. Examples include variants sporadically reported in the scientific literature, or stored in clinically-oriented online resources (e.g., OMIM) or in locus-specific databases (LSDBs). | LA26402-0 | ||
| Digital array The use of microfluidics and highly parallel real-time PCR to digitally count copy number in a sample. Similarly to other array-based techniques, uses comparative genomic hybridization. Rarely used, usually as a validation method. | LA26403-8 | ||
| FISH The use of multiple, differentially colored fluorescently-labeled probes (usu. fosmids, cosmids, or BACs) hybridized to a chromosome spread to detect copy number and position of target loci. Advantages: gives unambiuous relative positional information, can detect balanced and unbalanced translocations. Disadvantages: very low resolution, low throughput, labor intensive. | LA26404-6 | ||
| Gene expression array Similar to other array-based methods, except probes represent transcribed regions rather than the entire genome; therefore, subsequent intensity analysis reflects changes in gene expression which do not necessarily reflect changes in genomic DNA. Advantages: good for identifying possible gene deletions as a by-product of a gene expression experiment. Disadvantages: reduction or loss of signal does not necessarily indicate gene deletion - results must be followed up with more experiments. | LA26405-3 | ||
| Karyotyping May refer to any of several methods involving preparation of chromosome spreads and capable of detecting cytogenetic changes under a microscope. Examples are G-banding and fluorescence-based FISH, or chromosome "painting." | LA26406-1 | ||
| MAPH Multiplex Amplifiable Probe Hybridization; based on the quantitative recovery of short amplifiable probes after hybridization to genomic DNA. Advantages: good at detecting specific deletions in clinical samples; potential for high throughput. Rarely used. | LA26407-9 | ||
| MALDI-TOF MALDI-TOF mass spectroscopy of allele-specific primer extension products. Can be used to determine allele dosage ratios at specific loci in samples with heterozygous genotypes. Used rarely, as a validation method. | LA26408-7 | ||
| Merging | LA26808-8 | ||
| Multiple complete digestion Fosmids or other library inserts are fully digested with multiple restriction enzymes, and the resulting restriction pattern is compared to what is expected based on a reference. Used rarely, as a validation method. | LA26414-5 | ||
| MLPA Multiplex Ligation-dependent Probe Amplification; fluorescence- and capillary-based detection of copy number changes at specific loci using multiplex PCR. Advantages: low cost; not labor-intensive; excellent for detecting specific small copy number changes like exon duplications and deletions. | LA26415-2 | ||
| Optical mapping An integrated set of methods and analyses which involve stretching DNA into a single filament, immobilizing it on a charged surface, complete digestion with a single restriction enzyme, optical observation of the resulting restriction pattern, and comparison of results against the expected restriction pattern based on a reference genome. Advantages: ability to detect location and nature of insertions, deletions, and inversions. Disadvantages: highly specialized; cannot alone determine the sequence content or genomic origin of abberant events. | LA26417-8 | ||
| PCR The use of polymerase chain reaction technology to determine the presence or absence of a specified genomic locus. Advantages: easy; quick; inexpensive. Disadvantages: low throughput; low resolution. Typically used to genotype specific loci of interest. | LA26418-6 | ||
| qPCR (real-time PCR) Similar to PCR but fluorescence-based and able to detect copy number with some degree of accuracy. | LA26419-4 | ||
| ROMA Representational Oligonucleotide Microarray Analysis. Same as oligo aCGH except restriction digest and PCR amplification are applied to samples to reduce genomic complexity and thereby increase hybridization efficiency. | LA26420-2 | ||
| Denaturing high-pressure liquid chromatography (DHPLC) | LA26809-6 | ||
| DNA hybridization | LA26810-4 | ||
| Computational analysis | LA26811-2 | ||
| Single-stranded conformational polymorphism (SSCP) | LA26812-0 | ||
| Restriction fragment length polymorphism (RFLP) | LA26813-8 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Strukturální varianta metoda analýzy: |
| el-GR | Greek (Greece) | Μέθοδος ανάλυσης δομικών παραλλαγών: Synonyms: - * MOLPATH Nom Pt Type Ασθενής Δομική παραλλαγή Μέθοδος Μέθοδος ανάλυσης Μέθοδος ανάλυσης δομικών παραλλαγών |
| es-ES | Spanish (Spain) | Métodos de análisis de la variante estrucutral: |
| es-MX | Spanish (Mexico) | Método de análisis de variantes estructurales: |
| fr-FR | French (France) | Variant structurel méthode d'analyse: |
| it-IT | Italian (Italy) | Metodo di analisi della variante strutturale: Synonyms: Metodo di analisi Patologia molecolare paziente Punto nel tempo (episodio) |
| zh-CN | Chinese (China) | 结构变异分析方法: Synonyms: 分子病理学; |
53037-8 Genetic variation clinical significance [Imp]
Term Description
Single DNA marker or individual allele interpretation in the context of the assessed genetic disease.
Prior to the LOINC release 2.56 (June 2016), the answer list was updated per the recommendations of the American College of Medical Genetics (ACMG). The previous answer list number was LL603-2, and two of the answer strings and LA codes are the same in the new list (pathogenic and benign). In the new answer list, the presumed pathogenic, unknown significance and presumed benign answers from LL603-2 have been replaced by likely pathogenic, uncertain significance and likely benign. The answer strings and their respective LA codes from LL603-2 remain valid.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Genetic disease sequence variation interpretation
- Property
- Imp
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.24
- Last Updated
- Version 2.73 (MIN)
- Change Reason
- Updated LCN per CJM for HL7 CG IG
- Order vs. Observation
- Observation
- Common Test Rank Get Info
- 11949
Preferred Answer List LL4034-6
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Pathogenic | LA6668-3 | ||
| Likely pathogenic | LA26332-9 | ||
| Uncertain significance | LA26333-7 | ||
| Likely benign | LA26334-5 | ||
| Benign | LA6675-8 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 51975-1 | Individual allele results panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Genetické onemocnění sekvenční varianta identifikátor: |
| el-GR | Greek (Greece) | Ερμηνεία παραλλαγών αλληλουχίας γενετικών ασθενειών: Synonyms: HL7.GENETICS Imp Nom Pt Αίμα Αίμα/Ιστός Ερμηνεία Ερμηνεία παραλλαγών αλληλουχίας γενετικών ασθενειών Ιστός Μοριακή γενετική |
| es-ES | Spanish (Spain) | Interpretación de la variante de secuencia de la enfermedad genética: |
| es-MX | Spanish (Mexico) | Interpretación de la variación de la secuencia de la enfermedad genética: |
| fr-FR | French (France) | Maladie génétique interprétation globale de la variation de séquence: |
| it-IT | Italian (Italy) | Malattia genetica, interpretazione variazione di sequenza: Synonyms: Genetica molecolare Impressione/interpretazione di studio Interpretazione della variazione di sequenza di ma Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | genetische ziekte sequentievariatie interpretatie: Synonyms: molgen |
| pl-PL | Polish (Poland) | Interpretacja wariantów sekwencyjnych chorób genetycznych: Synonyms: diagnostyka molekularna Interpretacja wariantów sekwencyjnych w chorobach genetycznych wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Doença genética interpretação variação da seqüência: Synonyms: Interp; |
| ru-RU | Russian (Russian Federation) | Генетическое заболевание последовательность вариация интерпретация: Synonyms: Впечатление/интерпретация исследования Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Genetik hastalık sekans varyasyon yorumu: |
| zh-CN | Chinese (China) | 遗传性疾病序列变异解释: Synonyms: HL7 遗传学 全血或组织; |
69548-6 Genetic variant assessment
Term Description
Where testing scenarios are intended to assess the prescence or absence of a known set of DNA variants (e.g. tumor profiling using genotyping technology), then the Genetic Variant Assessment is used in conjunction with answer list supports structured communication of these findings. Of note, 'No Call' is different from 'Absent', because 'No Call' did not result in the determination of the marker's presents or absents. This may be due to test failure or specimen specific context which renders the test ineffective.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Genetic variant assessment
- Property
- Find
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.38
- Last Updated
- Version 2.73 (MIN)
- Order vs. Observation
- Observation
- Common Test Rank Get Info
- 13238
Preferred Answer List LL1971-2
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Present Copyright http://snomed.info/sct ID:52101004 Present (qualifier value) | LA9633-4 | ||
| Absent Copyright http://snomed.info/sct ID:2667000 Absent (qualifier value) | LA9634-2 | ||
| No call | LA18198-4 | ||
| Indeterminate Copyright http://snomed.info/sct ID:82334004 Indeterminate (qualifier value) | LA11884-6 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 55233-1 | Genetic analysis master panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Genetická varianta posouzení: |
| el-GR | Greek (Greece) | Αξιολόγηση γενετικών παραλλαγών: Synonyms: HL7.GENETICS Nom Pt Αίμα Αίμα/Ιστός Αξιολόγηση Αξιολόγηση γενετικών παραλλαγών Εύρεση Ιστός Μοριακή γενετική |
| es-ES | Spanish (Spain) | Valoración de la variabilidad genética: |
| es-MX | Spanish (Mexico) | Evaluación de variantes genéticas: |
| fr-FR | French (France) | Variant génétique étudié: |
| it-IT | Italian (Italy) | Variante genetica, valutazione: Synonyms: Genetica molecolare Osservazione Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | genetische variant evaluatie: Synonyms: molgen |
| pl-PL | Polish (Poland) | Ocena wariantu genetycznego: Synonyms: diagnostyka molekularna wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Variante genética avaliação: |
| ru-RU | Russian (Russian Federation) | Генетического варианта исследование: Synonyms: Генетического варианта определение Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Genetik varyant değerlendirme: |
| zh-CN | Chinese (China) | 遗传变异评估: Synonyms: HL7 遗传学 全血或组织; |
Third Party Copyright
This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. "SNOMED" and "SNOMED CT" are registered trademarks of the IHTSDO.
This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.
Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to https://www.snomed.org/get-snomed or [email protected]<mailto:[email protected]>. This may incur a fee in SNOMED International non-Member countries.
81259-4 Associated phenotype
Term Description
The possible phenotype associated with the genetic variant found in this study.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Associated phenotype
- Property
- Find
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.71 (MIN)
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Asociovaný fenotyp: |
| el-GR | Greek (Greece) | Συνδεδεμένος φαινότυπος: Synonyms: - MOLPATH Nom Pt Ασθενής Εύρεση Συνδεδεμένος φαινότυπος |
| es-ES | Spanish (Spain) | Fenotipo asociado probable: |
| es-MX | Spanish (Mexico) | Fenotipo asociado: |
| fr-FR | French (France) | Phénotype associé: |
| it-IT | Italian (Italy) | Probabile fenotipo associato: Synonyms: Osservazione Patologia molecolare paziente Punto nel tempo (episodio) |
| pl-PL | Polish (Poland) | Powiązany fenotyp: Synonyms: Fenotyp towarzyszący wynik kategorialny |
| zh-CN | Chinese (China) | 关联表型: Synonyms: 关联（相关、 |
53034-5 Allelic state
Term Description
The level of occurrence of a single DNA Marker within a set of chromosomes. Heterozygous indicates the DNA Marker is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Marker is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Marker exists in the only single copy of a gene in a non-homologous chromosome (The male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Marker is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Maker is present in all of the copies of mitochondrial DNA.
Observation Required in Panel
Conditional
Fully-Specified Name
- Component
- Allelic state
- Property
- Find
- Time
- Pt
- System
- Bld/Tiss
- Scale
- Nom
- Method
- Molgen
Basic Attributes
- Class
- HL7.GENETICS
- Type
- Laboratory
- First Released
- Version 2.24
- Last Updated
- Version 2.68 (MIN)
- Order vs. Observation
- Observation
Preferred Answer List LL381-5
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Heteroplasmic | LA6703-8 | ||
| Homoplasmic | LA6704-6 | ||
| Homozygous | LA6705-3 | ||
| Heterozygous | LA6706-1 | ||
| Hemizygous | LA6707-9 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 51960-3 | DNA marker results panel |
| 55233-1 | Genetic analysis master panel |
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Alelický stav: |
| el-GR | Greek (Greece) | Κατάσταση αλληλομόρφων: Synonyms: HL7.GENETICS Nom Pt Αίμα Αίμα/Ιστός Εύρεση Ιστός Κατάσταση Κατάσταση αλληλομόρφων Μοριακή γενετική |
| es-ES | Spanish (Spain) | Estado alélico: |
| es-MX | Spanish (Mexico) | Estado alélico: |
| fr-FR | French (France) | Statut allélique: |
| it-IT | Italian (Italy) | Stato allelico: Synonyms: Genetica molecolare Osservazione Punto nel tempo (episodio) Referto clinico di test genetico Sangue Sangue o Tessuto Tessuto & |
| nl-NL | Dutch (Netherlands) | allelstatus: Synonyms: molgen |
| pl-PL | Polish (Poland) | Status alleliczny: Synonyms: diagnostyka molekularna wynik kategorialny |
| pt-BR | Portuguese (Brazil) | Estado alélicas: Synonyms: Finding; |
| ru-RU | Russian (Russian Federation) | Аллельное состояние: Synonyms: Кровь Кровь или Ткань Номинальный; |
| tr-TR | Turkish (Turkey) | Allelik durum: |
| zh-CN | Chinese (China) | 等位状态: Synonyms: HL7 遗传学 全血或组织; |
81258-6 Sample variant allelic frequency [NFr]
Term Description
The fraction of all reads in a study sample at a given genomic locus that identify the allele (variant) in question. For homozygotes it will be close to 1.0; for heterozygotes it will be close to 0.5. It can be less than 0.5 in the case of mosaics or multiple chromosome, or mixtures of tumor cells and normal cells. This measure is an attribute of the variant and applies when the method is a Next Generation Sequencing (NGS) or similar. Such methods provide many reads from the sample for each locus. To report population allelic frequency, see LOINC 92821-8.
Allelic frequency is usually reported as a decimal fraction for both Sample Variant Allelic Frequency and Population Allelic Frequency, although it is occasionally reported as a percent. Special care/caution should be taken when reporting and converting to a decimal fraction.
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Sample variant allelic frequency
- Property
- NFr
- Time
- Pt
- System
- ^Patient
- Scale
- Qn
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.73 (MIN)
- Change Reason
- Updated Component from "Allelic frequency" to clarify that this term represents the allelic frequency within a study sample, and corrected Term description to describe sample-level allelic frequency rather than population allelic frequency.
- Order vs. Observation
- Observation
- Common Test Rank Get Info
- 8648
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Frekvence alelické varinty vzorek: |
| el-GR | Greek (Greece) | Συχνότητα αλληλόμορφων παραλλαγών δείγματος: Synonyms: - MOLPATH NFr Pt Qn Ασθενής Συχνότητα Συχνότητα αλληλομόρφων Συχνότητα αλληλόμορφων παραλλαγών δείγματος |
| es-ES | Spanish (Spain) | Frecuencia alélica variante de muestra: Synonyms: Cuantitativo |
| es-MX | Spanish (Mexico) | Frecuencia alélica variante de muestra: |
| fr-FR | French (France) | Example de fréquence de variant allélique: |
| it-IT | Italian (Italy) | Frequenza allelica della variante campione: Synonyms: Frazione numerica Patologia molecolare paziente Punto nel tempo (episodio) |
| zh-CN | Chinese (China) | 样品等位基因频率: Synonyms: 分子病理学; |
Example Units
| Unit | Source |
|---|---|
| % | Example UCUM Units |
82121-5 Allelic read depth
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Allelic read depth
- Property
- Num
- Time
- Pt
- System
- ^Patient
- Scale
- Qn
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.58 (MIN)
- Order vs. Observation
- Observation
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Hloubka čtení alel: |
| el-GR | Greek (Greece) | Βάθος ανάγνωσης αλληλομόρφων: Synonyms: - MOLPATH Pt Qn Αρ. Ασθενής Βάθος Βάθος ανάγνωσης αλληλομόρφων |
| es-ES | Spanish (Spain) | Profundidad de lectura alélica: Synonyms: Cuantitativo |
| es-MX | Spanish (Mexico) | Profundidad de lectura alélica: |
| fr-FR | French (France) | Profondeur allélique: |
| it-IT | Italian (Italy) | profondità di lettura allelica,genomico, SNPs, polimorfismi: Synonyms: Numero (conta) Patologia molecolare paziente Punto nel tempo (episodio) |
| pl-PL | Polish (Poland) | Głębokość odczytu allelu: Synonyms: Głębokość odczytu wariantu |
| zh-CN | Chinese (China) | 等位基因读取深度: Synonyms: 个数; |
Example Units
| Unit | Source |
|---|---|
| {#} | Example UCUM Units |
82120-7 Allelic phase
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Allelic phase
- Property
- Type
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.56
- Last Updated
- Version 2.58 (MIN)
- Order vs. Observation
- Observation
Example Answer List LL4025-4
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| 1st set of variants in cis relation to each other | LA26814-6 | ||
| 2nd set of variants in cis relation to each other | LA26815-3 | ||
| 3rd set of variants in cis relation to each other | LA26816-1 | ||
| 4th set of variants in cis relation to each other | LA26817-9 | ||
| 5th set of variants in cis relation to each other | LA26818-7 | ||
| Maternal | LA26320-4 | ||
| Paternal | LA26321-2 | ||
| Unknown Copyright http://snomed.info/sct ID:261665006 Unknown (qualifier value) | LA4489-6 | ||
| Other, Please specify: | LA46-8 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Alelická fáze: |
| el-GR | Greek (Greece) | Φάση αλληλομόρφων: Synonyms: - MOLPATH Nom Pt Type Ασθενής Φάση αλληλομόρφων |
| es-ES | Spanish (Spain) | Fase alélica: |
| es-MX | Spanish (Mexico) | Fase alélica: |
| fr-FR | French (France) | Phase allélique: |
| it-IT | Italian (Italy) | Fase allelica: Synonyms: Patologia molecolare paziente Punto nel tempo (episodio) |
| pl-PL | Polish (Poland) | Układ alleli: Synonyms: Konfiguracja alleli wynik kategorialny |
| zh-CN | Chinese (China) | 等位基因类型: Synonyms: 分子病理学; |
Third Party Copyright
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82309-6 Basis for allelic phase [Type]
Part Descriptions
LP220487-5 Basis for allelic phase
The evidential basis on which the allelic phase and/or the allelic state was concluded.
Choices include:
1) Directly measured;
2) Family DNA;
3) Family history;
4) Inferred from population data
Source: Regenstrief LOINC
Observation Required in Panel
Optional
Fully-Specified Name
- Component
- Basis for allelic phase
- Property
- Type
- Time
- Pt
- System
- ^Patient
- Scale
- Nom
- Method
- *
Basic Attributes
- Class
- MOLPATH
- Type
- Laboratory
- First Released
- Version 2.58
- Last Updated
- Version 2.58 (ADD)
- Order vs. Observation
- Observation
Example Answer List LL4050-2
| Answer | Code | Score | Answer ID |
|---|---|---|---|
| Directly measured | LA26426-9 | ||
| Family DNA | LA26427-7 | ||
| Family history | LA26428-5 | ||
| Inferred from population data | LA26429-3 |
Member of these Panels
| LOINC | Long Common Name |
|---|---|
| 81247-9 | Master HL7 genetic variant reporting panel |
Language Variants Get Info
| Tag | Language | Translation |
|---|---|---|
| cs-CZ | Czech (Czechia) | Základ pro alelickou fázi: |
| el-GR | Greek (Greece) | Βάση για φάση αλληλόμορφων: Synonyms: - * MOLPATH Nom Pt Type Ασθενής Βάση για φάση αλληλόμορφων Φάση αλληλομόρφων |
| es-ES | Spanish (Spain) | Bases para la fase alélica: |
| es-MX | Spanish (Mexico) | Base para la fase alélica: |
| fr-FR | French (France) | Bases de la phase allélique: |
| it-IT | Italian (Italy) | Fondamenti di fase allelica: Synonyms: Patologia molecolare paziente Punto nel tempo (episodio) |
| nl-NL | Dutch (Netherlands) | basis voor allelische fase: |
| pl-PL | Polish (Poland) | Podstawy na bazie której oceniany jest układ alleli: Synonyms: Konfiguracja alleli wynik kategorialny |
| zh-CN | Chinese (China) | 等位基因相的依据: Synonyms: 分子病理学; |