NHS North West Genomics
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Questionnaire: Master HL7 genetic variant reporting panel

Official URL: https://fhir.nwgenomics.nhs.uk/Questionnaire/81247-9 Version: 0.2.1
Draft as of 2026-03-21 Computable Name:

Master HL7 genetic variant reporting panel Questionnaire Viewer

Profile: Questionnaire

Structure
LinkIDTextCardinalityTypeDescription & Constraintsdoco
.. Questionnairehttps://fhir.nwgenomics.nhs.uk/Questionnaire/81247-9#0.2.1
... /81306-3Overall study variables type0..1groupValue Set:
.... /81306-3/53577-3Reason for study0..1stringValue Set:
..... /81306-3/53577-3-helpThe freeform text that is entered by the ordering provider to further annotate the coded Reason for Study [LOINC: 51967-8] associated with an ordered test. In HL7 v2 messages, OBR-31 should be used to report the reason for study.0..1displayValue Set:
.... /81306-3/51967-8Gene dis assessed0..1stringValue Set:
..... /81306-3/51967-8-helpCoded identifier of the disorder being assessed but with exception to allow the recording of something not included in the controlled vocabulary that is being used. Various coding systems may be used, including ICD-9-CM, ICD-10-CM, SCT and NCBI MedGen.0..1displayValue Set:
.... /81306-3/51963-7Medication assessed0..1stringValue Set:
..... /81306-3/51963-7-helpA coded medication assessed in a pharmacogenic test (recommend RxNorm)0..1displayValue Set:
.... /81306-3/48018-6Gene studied ID0..1stringValue Set:
..... /81306-3/48018-6-helpHUGO 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.0..1displayValue Set:
.... /81306-3/36908-2Gene Mut Tested Bld/T0..1stringValue Set:
..... /81306-3/36908-2-helpFor targeted mutation analysis, report the discrete mutations the study is designed to detect. In HL7 V2 they can be reported in one observation as a list separated by repeat delimiters OR as a series of separate OBX segments, one per mutation tested for. In FHIR, multiple coded entries can not be reported as a list in one observation value field. They must be reported as the values of separate observations.0..1displayValue Set:
.... /81306-3/51959-5DNA region of interest NumRange0..1stringValue Set:
..... /81306-3/51959-5-helpThis term is used to report the region(s) of interest for sequencing studies as one or more numeric ranges that identify the parts of the reference sequence that are sequenced. These can be recorded as one or more HL7 numeric ranges using repeat delimiters to seperate multiple such ranges. They can also be recorded singly, one per OBX, using OBX-4 to distinguish these repeats with the same Observation ID. However, such detailed specification of the sequencing region of interest is rare, in part because this information is often proprietary, and the region of interest is reported as a text description instead, e.g., "Sequenced all of the coding, and appropriate flanking regions," using [LOINC: 81293-3].0..1displayValue Set:
.... /81306-3/81293-3DNA range(s) examined Nar0..1stringValue Set:
..... /81306-3/81293-3-helpThis term is used to report a narrative description of the range(s) of DNA sequences examined in this sequencing study. Genetic test reports only rarely include explicit numeric ranges (which would be reported using [LOINC: 51959-5]) beause they are often proprietary, and more often describe the regions examined in narrative. For example, "all coding regions and appropriate flanking regions." To report the region of interest (e.g., in terms of introns and exons) rather than the specific DNA sequences examined, [LOINC: 47999-8] may be used.0..1displayValue Set:
.... /81306-3/51968-6Gene dis anl interp-Imp0..1choiceValue Set:
Options: 4 options
..... /81306-3/51968-6-helpInterpretation of all identified DNA Markers and/or Individual Alleles along with any known clinical information for the benefit of aiding clinicians in understanding the results overall. This is used for Symptomatic or Asymptomatic testing other than Carrier testing.0..1displayValue Set:
.... /81306-3/83006-7Del-dup interp Patient-Imp0..1choiceValue Set:
Options: 3 options
.... /81306-3/51969-4Gene analysis narr rpt Doc0..1stringValue Set:
..... /81306-3/51969-4-helpNarative report in disease diagnostic-based format.0..1displayValue Set:
.... /81306-3/81291-7Struct var ISCN name0..1stringValue Set:
..... /81306-3/81291-7-helpISCN is a syntax for describing cytogenetic findings, from classical karyotypes to details that can be observed with copy number methodologies. Using ISCN nomenclature is highly recommended for reporting structural variants.0..1displayValue Set:
.... /81306-3/62374-4Human ref seq assembly+build0..1choiceValue Set:
Options: 5 options
..... /81306-3/62374-4-helpThe NCBI build id for human genome assemblies.0..1displayValue Set:
.... /81306-3/81303-0HGVS version0..1stringValue Set:
..... /81306-3/81303-0-helpReport the version of HGVS used for all observations specified using HGVS nomenclature. Any change in the HGVS recommendations will get a new version number based on the date of the change. The format for reporting the HGVS version used is: <version #>.<date produced in YYMMDD format>, for example, 2.120831.0..1displayValue Set:
.... /81306-3/82115-7dbSNP version0..1stringValue Set:
.... /81306-3/83007-5COSMIC version0..1stringValue Set:
.... /81306-3/83008-3ClinVar version0..1stringValue Set:
... /81250-3Simple var pnl0..1groupValue Set:
.... /81250-3/83005-9Variant category0..1choiceValue Set:
Options: 2 options
.... /81250-3/81252-9Simple var ID0..1stringValue Set:
..... /81250-3/81252-9-helpThis 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/]0..1displayValue Set:
.... /81250-3/48018-6Gene studied ID0..1stringValue Set:
..... /81250-3/48018-6-helpHUGO 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.0..1displayValue Set:
.... /81250-3/51958-7Transcript ref sequence ID0..1stringValue Set:
..... /81250-3/51958-7-helpThis 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).0..1displayValue Set:
.... /81250-3/48004-6DNA change0..1stringValue Set:
..... /81250-3/48004-6-helpHuman 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.0..1displayValue Set:
.... /81250-3/48005-3Amino acid change0..1stringValue Set:
..... /81250-3/48005-3-helpHuman 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.0..1displayValue Set:
.... /81250-3/48019-4DNA Change Type0..1choiceValue Set:
Options: 17 options
..... /81250-3/48019-4-helpCodified 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.0..1displayValue Set:
.... /81250-3/48006-1Amino acid change type0..1choiceValue Set:
Options: 11 options
..... /81250-3/48006-1-helpCodified 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.0..1displayValue Set:
.... /81250-3/48013-7Genomic reference sequence ID0..1stringValue Set:
..... /81250-3/48013-7-helpThis 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 LRG0..1displayValue Set:
.... /81250-3/81290-9Struct var HGVS name0..1stringValue Set:
..... /81250-3/81290-9-helpThe name of a structural variant reported using HGVS nomenclature.0..1displayValue Set:
.... /81250-3/69547-8Ref nucleotide0..1stringValue Set:
..... /81250-3/69547-8-helpReference 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.0..1displayValue Set:
.... /81250-3/81254-5Gen allele loc ID0..1stringValue Set:
..... /81250-3/81254-5-helpThe 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/]0..1displayValue Set:
.... /81250-3/69551-0Alt allele0..1stringValue Set:
..... /81250-3/69551-0-helpThe 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.0..1displayValue Set:
.... /81250-3/84414-2Haplotype name Bld/T0..1stringValue Set:
.... /81250-3/81255-2dbSNP ID0..1stringValue Set:
..... /81250-3/81255-2-helpThe 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/]0..1displayValue Set:
.... /81250-3/81257-8CIGAR var ID0..1stringValue Set:
..... /81250-3/81257-8-helpThis 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.0..1displayValue Set:
.... /81250-3/48001-2Cyto loc ID0..1stringValue Set:
.... /81250-3/48002-0Genomic source class0..1choiceValue Set:
Options: 8 options
..... /81250-3/48002-0-helpThe genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.0..1displayValue Set:
.... /81250-3/81304-8Struct var analysis method0..1choiceValue Set:
Options: 23 options
..... /81250-3/81304-8-helpThe method used for analyzing chromosome structural variation, such as FISH, arrCGH, sequencing, and MLPA.0..1displayValue Set:
.... /81250-3/53037-8Gene dis seq var interp-Imp0..1choiceValue Set:
Options: 5 options
..... /81250-3/53037-8-helpSingle 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.0..1displayValue Set:
.... /81250-3/69548-6Genetic var assess0..1choiceValue Set:
Options: 4 options
..... /81250-3/69548-6-helpWhere 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.0..1displayValue Set:
.... /81250-3/81259-4Prob assoc phenotype0..1stringValue Set:
..... /81250-3/81259-4-helpThe possible phenotype associated with the genetic variant found in this study.0..1displayValue Set:
.... /81250-3/53034-5Allelic state0..1choiceValue Set:
Options: 5 options
..... /81250-3/53034-5-helpThe 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.0..1displayValue Set:
.... /81250-3/81258-6Sample VAF0..1decimalValue Set:
..... /81250-3/81258-6-helpThe 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.0..1displayValue Set:
.... /81250-3/82121-5Allelic read depth0..1decimalValue Set:
.... /81250-3/82120-7Allelic phase0..1choiceValue Set:
Options: 9 options
.... /81250-3/82309-6Basis allelic phase0..1choiceValue Set:
Options: 4 options
.... /81250-3-helpThis 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.0..1displayValue Set:
... /81297-4Struct variant pnl0..1groupValue Set:
.... /81297-4/82155-3Gen struct var copy num0..1decimalValue Set:
.... /81297-4/81299-0Struct var rep arrCGH Rto0..1decimalValue Set:
.... /81297-4/81300-6Struct var len0..1decimalValue Set:
..... /81297-4/81300-6-helpLength of the structural variant, which information may be ascertained in some but not all types of structural variants.0..1displayValue Set:
.... /81297-4/81301-4Struct var outer start-end NumRange0..1decimalValue Set:
..... /81297-4/81301-4-helpThe genomic coordinates of the widest genomic range in which the variant might reside.0..1displayValue Set:
.... /81297-4/81302-2Struct var inner start-end NumRange0..1decimalValue Set:
..... /81297-4/81302-2-helpThe genomic coordinates of the narrowest genomic range in which the variant might reside.0..1displayValue Set:
... /81251-1Comp var pnl0..1groupValue Set:
.... /81251-1/81260-2Comp var ID0..1stringValue Set:
..... /81251-1/81260-2-helpThis 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/]0..1displayValue Set:
.... /81251-1/81262-8Comp var HGVS name0..1stringValue Set:
..... /81251-1/81262-8-helpThis 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.0..1displayValue Set:
.... /81251-1/81263-6Comp var type0..1choiceValue Set:
Options: 4 options
..... /81251-1/81263-6-helpThe type of complex variant, for example, compound heterozygous or haplotype.0..1displayValue Set:
.... /81251-1/81259-4Prob assoc phenotype0..1stringValue Set:
..... /81251-1/81259-4-helpThe possible phenotype associated with the genetic variant found in this study.0..1displayValue Set:
.... /81251-1/53037-8Gene dis seq var interp-Imp0..1choiceValue Set:
Options: 5 options
..... /81251-1/53037-8-helpSingle 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.0..1displayValue Set:
.... /81251-1/53034-5Allelic state0..1choiceValue Set:
Options: 5 options
..... /81251-1/53034-5-helpThe 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.0..1displayValue Set:
.... /81251-1/82309-6Basis allelic phase0..1choiceValue Set:
Options: 4 options
.... /81251-1/81250-3Simple var pnl0..1groupValue Set:
..... /81251-1/81250-3/83005-9Variant category0..1choiceValue Set:
Options: 2 options
..... /81251-1/81250-3/81252-9Simple var ID0..1stringValue Set:
...... /81251-1/81250-3/81252-9-helpThis 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/]0..1displayValue Set:
..... /81251-1/81250-3/48018-6Gene studied ID0..1stringValue Set:
...... /81251-1/81250-3/48018-6-helpHUGO 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.0..1displayValue Set:
..... /81251-1/81250-3/51958-7Transcript ref sequence ID0..1stringValue Set:
...... /81251-1/81250-3/51958-7-helpThis 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).0..1displayValue Set:
..... /81251-1/81250-3/48004-6DNA change0..1stringValue Set:
...... /81251-1/81250-3/48004-6-helpHuman 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.0..1displayValue Set:
..... /81251-1/81250-3/48005-3Amino acid change0..1stringValue Set:
...... /81251-1/81250-3/48005-3-helpHuman 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.0..1displayValue Set:
..... /81251-1/81250-3/48019-4DNA Change Type0..1choiceValue Set:
Options: 17 options
...... /81251-1/81250-3/48019-4-helpCodified 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.0..1displayValue Set:
..... /81251-1/81250-3/48006-1Amino acid change type0..1choiceValue Set:
Options: 11 options
...... /81251-1/81250-3/48006-1-helpCodified 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.0..1displayValue Set:
..... /81251-1/81250-3/48013-7Genomic reference sequence ID0..1stringValue Set:
...... /81251-1/81250-3/48013-7-helpThis 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 LRG0..1displayValue Set:
..... /81251-1/81250-3/81290-9Struct var HGVS name0..1stringValue Set:
...... /81251-1/81250-3/81290-9-helpThe name of a structural variant reported using HGVS nomenclature.0..1displayValue Set:
..... /81251-1/81250-3/69547-8Ref nucleotide0..1stringValue Set:
...... /81251-1/81250-3/69547-8-helpReference 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.0..1displayValue Set:
..... /81251-1/81250-3/81254-5Gen allele loc ID0..1stringValue Set:
...... /81251-1/81250-3/81254-5-helpThe 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/]0..1displayValue Set:
..... /81251-1/81250-3/69551-0Alt allele0..1stringValue Set:
...... /81251-1/81250-3/69551-0-helpThe 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.0..1displayValue Set:
..... /81251-1/81250-3/84414-2Haplotype name Bld/T0..1stringValue Set:
..... /81251-1/81250-3/81255-2dbSNP ID0..1stringValue Set:
...... /81251-1/81250-3/81255-2-helpThe 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/]0..1displayValue Set:
..... /81251-1/81250-3/81257-8CIGAR var ID0..1stringValue Set:
...... /81251-1/81250-3/81257-8-helpThis 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.0..1displayValue Set:
..... /81251-1/81250-3/48001-2Cyto loc ID0..1stringValue Set:
..... /81251-1/81250-3/48002-0Genomic source class0..1choiceValue Set:
Options: 8 options
...... /81251-1/81250-3/48002-0-helpThe genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.0..1displayValue Set:
..... /81251-1/81250-3/81304-8Struct var analysis method0..1choiceValue Set:
Options: 23 options
...... /81251-1/81250-3/81304-8-helpThe method used for analyzing chromosome structural variation, such as FISH, arrCGH, sequencing, and MLPA.0..1displayValue Set:
..... /81251-1/81250-3/53037-8Gene dis seq var interp-Imp0..1choiceValue Set:
Options: 5 options
...... /81251-1/81250-3/53037-8-helpSingle 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.0..1displayValue Set:
..... /81251-1/81250-3/69548-6Genetic var assess0..1choiceValue Set:
Options: 4 options
...... /81251-1/81250-3/69548-6-helpWhere 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.0..1displayValue Set:
..... /81251-1/81250-3/81259-4Prob assoc phenotype0..1stringValue Set:
...... /81251-1/81250-3/81259-4-helpThe possible phenotype associated with the genetic variant found in this study.0..1displayValue Set:
..... /81251-1/81250-3/53034-5Allelic state0..1choiceValue Set:
Options: 5 options
...... /81251-1/81250-3/53034-5-helpThe 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.0..1displayValue Set:
..... /81251-1/81250-3/81258-6Sample VAF0..1decimalValue Set:
...... /81251-1/81250-3/81258-6-helpThe 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.0..1displayValue Set:
..... /81251-1/81250-3/82121-5Allelic read depth0..1decimalValue Set:
..... /81251-1/81250-3/82120-7Allelic phase0..1choiceValue Set:
Options: 9 options
..... /81251-1/81250-3/82309-6Basis allelic phase0..1choiceValue Set:
Options: 4 options
..... /81251-1/81250-3-helpThis 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.0..1displayValue Set:
.... /81251-1-helpThis panel is used to report information related to a complex genetic variant and includes a repeating subpanel for reporting specific information for each simple variation that the complex variant includes.0..1displayValue Set:
... /82118-1Pharmg result pnl0..1groupValue Set:
.... /82118-1/48018-6Gene studied ID0..1stringValue Set:
..... /82118-1/48018-6-helpHUGO 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.0..1displayValue Set:
.... /82118-1/84413-4Genotype name Patient0..1stringValue Set:
.... /82118-1/53040-2Drug metab seq var interp-Imp0..1choiceValue Set:
Options: 5 options
..... /82118-1/53040-2-helpPredicted phenotype for drug efficacy. A single marker interpretation value known to allow (responsive) or prevent (resistant) the drug to perform. Prior to the LOINC release 2.56 (June 2016), the answer list was updated per the recommendations of the Clinical Pharmacogenetics Implementation Consortium (CPIC). The previous answer list number was LL609-9, and three of the answer strings and LA codes are the same in the new list (ultrarapid metabolizer, intermediate metabolizer, and poor metabolizer). In the new answer list, the extensive metabolizer answer (LA10316-0) from LL609-9 has been replaced with two new answers (rapid metabolizer, normal metabolizer). LA10316-0 is still a valid LA code for the "extensive metabolizer" answer string.0..1displayValue Set:
.... /82118-1/51961-1Drug eff seq var interp-Imp0..1choiceValue Set:
Options: 8 options
..... /82118-1/51961-1-helpPredicted phenotype for ability of drug to bind to intended site in order to deliver intended affect. A single marker interpretation value known to allow (responsive) or prevent (resistant) the drug to perform.0..1displayValue Set:
.... /82118-1/83009-1Genetic var eff high-risk allele0..1choiceValue Set:
Options: 2 options
.... /82118-1/82117-3Med usage impl pnl0..1groupValue Set:
..... /82118-1/82117-3/51963-7Medication assessed0..1stringValue Set:
...... /82118-1/82117-3/51963-7-helpA coded medication assessed in a pharmacogenic test (recommend RxNorm)0..1displayValue Set:
..... /82118-1/82117-3/82116-5Med usage sugg0..1choiceValue Set:
Options: 5 options
..... /82118-1/82117-3/83010-9Med usage sugg Patient-Imp0..1stringValue Set:
... /83011-7Haplotype definition Pnl0..1groupValue Set:
.... /83011-7/48018-6Gene studied ID0..1stringValue Set:
..... /83011-7/48018-6-helpHUGO 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.0..1displayValue Set:
.... /83011-7/84414-2Haplotype name Bld/T0..1stringValue Set:
.... /83011-7/81250-3Simple var pnl0..1groupValue Set:
..... /83011-7/81250-3/83005-9Variant category0..1choiceValue Set:
Options: 2 options
..... /83011-7/81250-3/81252-9Simple var ID0..1stringValue Set:
...... /83011-7/81250-3/81252-9-helpThis 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/]0..1displayValue Set:
..... /83011-7/81250-3/48018-6Gene studied ID0..1stringValue Set:
...... /83011-7/81250-3/48018-6-helpHUGO 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.0..1displayValue Set:
..... /83011-7/81250-3/51958-7Transcript ref sequence ID0..1stringValue Set:
...... /83011-7/81250-3/51958-7-helpThis 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).0..1displayValue Set:
..... /83011-7/81250-3/48004-6DNA change0..1stringValue Set:
...... /83011-7/81250-3/48004-6-helpHuman 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.0..1displayValue Set:
..... /83011-7/81250-3/48005-3Amino acid change0..1stringValue Set:
...... /83011-7/81250-3/48005-3-helpHuman 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.0..1displayValue Set:
..... /83011-7/81250-3/48019-4DNA Change Type0..1choiceValue Set:
Options: 17 options
...... /83011-7/81250-3/48019-4-helpCodified 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.0..1displayValue Set:
..... /83011-7/81250-3/48006-1Amino acid change type0..1choiceValue Set:
Options: 11 options
...... /83011-7/81250-3/48006-1-helpCodified 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.0..1displayValue Set:
..... /83011-7/81250-3/48013-7Genomic reference sequence ID0..1stringValue Set:
...... /83011-7/81250-3/48013-7-helpThis 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 LRG0..1displayValue Set:
..... /83011-7/81250-3/81290-9Struct var HGVS name0..1stringValue Set:
...... /83011-7/81250-3/81290-9-helpThe name of a structural variant reported using HGVS nomenclature.0..1displayValue Set:
..... /83011-7/81250-3/69547-8Ref nucleotide0..1stringValue Set:
...... /83011-7/81250-3/69547-8-helpReference 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.0..1displayValue Set:
..... /83011-7/81250-3/81254-5Gen allele loc ID0..1stringValue Set:
...... /83011-7/81250-3/81254-5-helpThe 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/]0..1displayValue Set:
..... /83011-7/81250-3/69551-0Alt allele0..1stringValue Set:
...... /83011-7/81250-3/69551-0-helpThe 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.0..1displayValue Set:
..... /83011-7/81250-3/84414-2Haplotype name Bld/T0..1stringValue Set:
..... /83011-7/81250-3/81255-2dbSNP ID0..1stringValue Set:
...... /83011-7/81250-3/81255-2-helpThe 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/]0..1displayValue Set:
..... /83011-7/81250-3/81257-8CIGAR var ID0..1stringValue Set:
...... /83011-7/81250-3/81257-8-helpThis 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.0..1displayValue Set:
..... /83011-7/81250-3/48001-2Cyto loc ID0..1stringValue Set:
..... /83011-7/81250-3/48002-0Genomic source class0..1choiceValue Set:
Options: 8 options
...... /83011-7/81250-3/48002-0-helpThe genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.0..1displayValue Set:
..... /83011-7/81250-3/81304-8Struct var analysis method0..1choiceValue Set:
Options: 23 options
...... /83011-7/81250-3/81304-8-helpThe method used for analyzing chromosome structural variation, such as FISH, arrCGH, sequencing, and MLPA.0..1displayValue Set:
..... /83011-7/81250-3/53037-8Gene dis seq var interp-Imp0..1choiceValue Set:
Options: 5 options
...... /83011-7/81250-3/53037-8-helpSingle 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.0..1displayValue Set:
..... /83011-7/81250-3/69548-6Genetic var assess0..1choiceValue Set:
Options: 4 options
...... /83011-7/81250-3/69548-6-helpWhere 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.0..1displayValue Set:
..... /83011-7/81250-3/81259-4Prob assoc phenotype0..1stringValue Set:
...... /83011-7/81250-3/81259-4-helpThe possible phenotype associated with the genetic variant found in this study.0..1displayValue Set:
..... /83011-7/81250-3/53034-5Allelic state0..1choiceValue Set:
Options: 5 options
...... /83011-7/81250-3/53034-5-helpThe 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.0..1displayValue Set:
..... /83011-7/81250-3/81258-6Sample VAF0..1decimalValue Set:
...... /83011-7/81250-3/81258-6-helpThe 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.0..1displayValue Set:
..... /83011-7/81250-3/82121-5Allelic read depth0..1decimalValue Set:
..... /83011-7/81250-3/82120-7Allelic phase0..1choiceValue Set:
Options: 9 options
..... /83011-7/81250-3/82309-6Basis allelic phase0..1choiceValue Set:
Options: 4 options
..... /83011-7/81250-3-helpThis 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.0..1displayValue Set:

doco Documentation for this format

Options Sets

Answer options for /81306-3/51968-6

  • http://loinc.org#LA6576-8 ("Positive")
  • http://loinc.org#LA6577-6 ("Negative")
  • http://loinc.org#LA9663-1 ("Inconclusive")
  • http://loinc.org#LA9664-9 ("Failure")

Answer options for /81306-3/83006-7

  • http://loinc.org#LA26803-9 ("No deletion or duplication detected in studied region")
  • http://loinc.org#LA26804-7 ("Deletion and/or duplication detected in studied regions")
  • http://loinc.org#LA9663-1 ("Inconclusive")

Answer options for /81306-3/62374-4

  • http://loinc.org#LA14032-9 ("NCBI Build 34")
  • http://loinc.org#LA14029-5 ("GRCh37")
  • http://loinc.org#LA14030-3 ("NCBI Build 36.1")
  • http://loinc.org#LA14031-1 ("NCBI Build 35")
  • http://loinc.org#LA26806-2 ("GRCh38")

Answer options for /81250-3/83005-9

  • http://loinc.org#LA26801-3 ("Simple variant")
  • http://loinc.org#LA26802-1 ("Structural variant")

Answer options for /81250-3/48019-4

  • http://loinc.org#LA9658-1 ("Wild type")
  • http://loinc.org#LA6692-3 ("Deletion")
  • http://loinc.org#LA6686-5 ("Duplication")
  • http://loinc.org#LA6687-3 ("Insertion")
  • http://loinc.org#LA6688-1 ("Insertion/Deletion")
  • http://loinc.org#LA6689-9 ("Inversion")
  • http://loinc.org#LA6690-7 ("Substitution")
  • http://loinc.org#LA14033-7 ("Copy number gain")
  • http://loinc.org#LA14034-5 ("Copy number loss")
  • http://loinc.org#LA26324-6 ("Mobile element insertion")
  • http://loinc.org#LA26325-3 ("Novel sequence insertion")
  • http://loinc.org#LA26326-1 ("Tandem duplication")
  • http://loinc.org#LA26327-9 ("Intrachromosomal breakpoint")
  • http://loinc.org#LA26328-7 ("Interchromosomal breakpoint")
  • http://loinc.org#LA26331-1 ("Translocation")
  • http://loinc.org#LA26330-3 ("Complex")
  • http://loinc.org#LA26329-5 ("Sequence alteration")

Answer options for /81250-3/48006-1

  • http://loinc.org#LA9658-1 ("Wild type")
  • http://loinc.org#LA6692-3 ("Deletion")
  • http://loinc.org#LA6686-5 ("Duplication")
  • http://loinc.org#LA6694-9 ("Frameshift")
  • http://loinc.org#LA6695-6 ("Initiating Methionine")
  • http://loinc.org#LA6687-3 ("Insertion")
  • http://loinc.org#LA9659-9 ("Insertion and Deletion")
  • http://loinc.org#LA6698-0 ("Missense")
  • http://loinc.org#LA6699-8 ("Nonsense")
  • http://loinc.org#LA6700-4 ("Silent")
  • http://loinc.org#LA6701-2 ("Stop Codon Mutation")

Answer options for /81250-3/48002-0

  • http://loinc.org#LA6683-2 ("Germline")
  • http://loinc.org#LA6684-0 ("Somatic")
  • http://loinc.org#LA10429-1 ("Fetal")
  • http://loinc.org#LA18194-3 ("Likely germline")
  • http://loinc.org#LA18195-0 ("Likely somatic")
  • http://loinc.org#LA18196-8 ("Likely fetal")
  • http://loinc.org#LA18197-6 ("Unknown genomic origin")
  • http://loinc.org#LA26807-0 ("De novo")

Answer options for /81250-3/81304-8

  • http://loinc.org#LA26398-0 ("Sequencing")
  • http://loinc.org#LA26399-8 ("Oligo aCGH")
  • http://loinc.org#LA26400-4 ("SNP array")
  • http://loinc.org#LA26401-2 ("BAC aCGH")
  • http://loinc.org#LA26402-0 ("Curated")
  • http://loinc.org#LA26403-8 ("Digital array")
  • http://loinc.org#LA26404-6 ("FISH")
  • http://loinc.org#LA26405-3 ("Gene expression array")
  • http://loinc.org#LA26406-1 ("Karyotyping")
  • http://loinc.org#LA26407-9 ("MAPH")
  • http://loinc.org#LA26408-7 ("MALDI-TOF")
  • http://loinc.org#LA26808-8 ("Merging")
  • http://loinc.org#LA26414-5 ("Multiple complete digestion")
  • http://loinc.org#LA26415-2 ("MLPA")
  • http://loinc.org#LA26417-8 ("Optical mapping")
  • http://loinc.org#LA26418-6 ("PCR")
  • http://loinc.org#LA26419-4 ("qPCR (real-time PCR)")
  • http://loinc.org#LA26420-2 ("ROMA")
  • http://loinc.org#LA26809-6 ("Denaturing high-pressure liquid chromatography (DHPLC)")
  • http://loinc.org#LA26810-4 ("DNA hybridization")
  • http://loinc.org#LA26811-2 ("Computational analysis")
  • http://loinc.org#LA26812-0 ("Single-stranded conformational polymorphism (SSCP)")
  • http://loinc.org#LA26813-8 ("Restriction fragment length polymorphism (RFLP)")

Answer options for /81250-3/53037-8

  • http://loinc.org#LA6668-3 ("Pathogenic")
  • http://loinc.org#LA26332-9 ("Likely pathogenic")
  • http://loinc.org#LA26333-7 ("Uncertain significance")
  • http://loinc.org#LA26334-5 ("Likely benign")
  • http://loinc.org#LA6675-8 ("Benign")

Answer options for /81250-3/69548-6

  • http://loinc.org#LA9633-4 ("Present")
  • http://loinc.org#LA9634-2 ("Absent")
  • http://loinc.org#LA18198-4 ("No call")
  • http://loinc.org#LA11884-6 ("Indeterminate")

Answer options for /81250-3/53034-5

  • http://loinc.org#LA6703-8 ("Heteroplasmic")
  • http://loinc.org#LA6704-6 ("Homoplasmic")
  • http://loinc.org#LA6705-3 ("Homozygous")
  • http://loinc.org#LA6706-1 ("Heterozygous")
  • http://loinc.org#LA6707-9 ("Hemizygous")

Answer options for /81250-3/82120-7

  • http://loinc.org#LA26814-6 ("1st set of variants in cis relation to each other")
  • http://loinc.org#LA26815-3 ("2nd set of variants in cis relation to each other")
  • http://loinc.org#LA26816-1 ("3rd set of variants in cis relation to each other")
  • http://loinc.org#LA26817-9 ("4th set of variants in cis relation to each other")
  • http://loinc.org#LA26818-7 ("5th set of variants in cis relation to each other")
  • http://loinc.org#LA26320-4 ("Maternal")
  • http://loinc.org#LA26321-2 ("Paternal")
  • http://loinc.org#LA4489-6 ("Unknown")
  • http://loinc.org#LA46-8 ("Other")

Answer options for /81250-3/82309-6

  • http://loinc.org#LA26426-9 ("Directly measured")
  • http://loinc.org#LA26427-7 ("Family DNA")
  • http://loinc.org#LA26428-5 ("Family history")
  • http://loinc.org#LA26429-3 ("Inferred from population data")

Answer options for /81251-1/81263-6

  • http://loinc.org#LA26217-2 ("Compound heterozygous")
  • http://loinc.org#LA26220-6 ("Double heterozygous")
  • http://loinc.org#LA26218-0 ("Haplotype")
  • http://loinc.org#LA6707-9 ("Hemizygous")

Answer options for /81251-1/53037-8

  • http://loinc.org#LA6668-3 ("Pathogenic")
  • http://loinc.org#LA26332-9 ("Likely pathogenic")
  • http://loinc.org#LA26333-7 ("Uncertain significance")
  • http://loinc.org#LA26334-5 ("Likely benign")
  • http://loinc.org#LA6675-8 ("Benign")

Answer options for /81251-1/53034-5

  • http://loinc.org#LA6703-8 ("Heteroplasmic")
  • http://loinc.org#LA6704-6 ("Homoplasmic")
  • http://loinc.org#LA6705-3 ("Homozygous")
  • http://loinc.org#LA6706-1 ("Heterozygous")
  • http://loinc.org#LA6707-9 ("Hemizygous")

Answer options for /81251-1/82309-6

  • http://loinc.org#LA26426-9 ("Directly measured")
  • http://loinc.org#LA26427-7 ("Family DNA")
  • http://loinc.org#LA26428-5 ("Family history")
  • http://loinc.org#LA26429-3 ("Inferred from population data")

Answer options for /81251-1/81250-3/83005-9

  • http://loinc.org#LA26801-3 ("Simple variant")
  • http://loinc.org#LA26802-1 ("Structural variant")

Answer options for /81251-1/81250-3/48019-4

  • http://loinc.org#LA9658-1 ("Wild type")
  • http://loinc.org#LA6692-3 ("Deletion")
  • http://loinc.org#LA6686-5 ("Duplication")
  • http://loinc.org#LA6687-3 ("Insertion")
  • http://loinc.org#LA6688-1 ("Insertion/Deletion")
  • http://loinc.org#LA6689-9 ("Inversion")
  • http://loinc.org#LA6690-7 ("Substitution")
  • http://loinc.org#LA14033-7 ("Copy number gain")
  • http://loinc.org#LA14034-5 ("Copy number loss")
  • http://loinc.org#LA26324-6 ("Mobile element insertion")
  • http://loinc.org#LA26325-3 ("Novel sequence insertion")
  • http://loinc.org#LA26326-1 ("Tandem duplication")
  • http://loinc.org#LA26327-9 ("Intrachromosomal breakpoint")
  • http://loinc.org#LA26328-7 ("Interchromosomal breakpoint")
  • http://loinc.org#LA26331-1 ("Translocation")
  • http://loinc.org#LA26330-3 ("Complex")
  • http://loinc.org#LA26329-5 ("Sequence alteration")

Answer options for /81251-1/81250-3/48006-1

  • http://loinc.org#LA9658-1 ("Wild type")
  • http://loinc.org#LA6692-3 ("Deletion")
  • http://loinc.org#LA6686-5 ("Duplication")
  • http://loinc.org#LA6694-9 ("Frameshift")
  • http://loinc.org#LA6695-6 ("Initiating Methionine")
  • http://loinc.org#LA6687-3 ("Insertion")
  • http://loinc.org#LA9659-9 ("Insertion and Deletion")
  • http://loinc.org#LA6698-0 ("Missense")
  • http://loinc.org#LA6699-8 ("Nonsense")
  • http://loinc.org#LA6700-4 ("Silent")
  • http://loinc.org#LA6701-2 ("Stop Codon Mutation")

Answer options for /81251-1/81250-3/48002-0

  • http://loinc.org#LA6683-2 ("Germline")
  • http://loinc.org#LA6684-0 ("Somatic")
  • http://loinc.org#LA10429-1 ("Fetal")
  • http://loinc.org#LA18194-3 ("Likely germline")
  • http://loinc.org#LA18195-0 ("Likely somatic")
  • http://loinc.org#LA18196-8 ("Likely fetal")
  • http://loinc.org#LA18197-6 ("Unknown genomic origin")
  • http://loinc.org#LA26807-0 ("De novo")

Answer options for /81251-1/81250-3/81304-8

  • http://loinc.org#LA26398-0 ("Sequencing")
  • http://loinc.org#LA26399-8 ("Oligo aCGH")
  • http://loinc.org#LA26400-4 ("SNP array")
  • http://loinc.org#LA26401-2 ("BAC aCGH")
  • http://loinc.org#LA26402-0 ("Curated")
  • http://loinc.org#LA26403-8 ("Digital array")
  • http://loinc.org#LA26404-6 ("FISH")
  • http://loinc.org#LA26405-3 ("Gene expression array")
  • http://loinc.org#LA26406-1 ("Karyotyping")
  • http://loinc.org#LA26407-9 ("MAPH")
  • http://loinc.org#LA26408-7 ("MALDI-TOF")
  • http://loinc.org#LA26808-8 ("Merging")
  • http://loinc.org#LA26414-5 ("Multiple complete digestion")
  • http://loinc.org#LA26415-2 ("MLPA")
  • http://loinc.org#LA26417-8 ("Optical mapping")
  • http://loinc.org#LA26418-6 ("PCR")
  • http://loinc.org#LA26419-4 ("qPCR (real-time PCR)")
  • http://loinc.org#LA26420-2 ("ROMA")
  • http://loinc.org#LA26809-6 ("Denaturing high-pressure liquid chromatography (DHPLC)")
  • http://loinc.org#LA26810-4 ("DNA hybridization")
  • http://loinc.org#LA26811-2 ("Computational analysis")
  • http://loinc.org#LA26812-0 ("Single-stranded conformational polymorphism (SSCP)")
  • http://loinc.org#LA26813-8 ("Restriction fragment length polymorphism (RFLP)")

Answer options for /81251-1/81250-3/53037-8

  • http://loinc.org#LA6668-3 ("Pathogenic")
  • http://loinc.org#LA26332-9 ("Likely pathogenic")
  • http://loinc.org#LA26333-7 ("Uncertain significance")
  • http://loinc.org#LA26334-5 ("Likely benign")
  • http://loinc.org#LA6675-8 ("Benign")

Answer options for /81251-1/81250-3/69548-6

  • http://loinc.org#LA9633-4 ("Present")
  • http://loinc.org#LA9634-2 ("Absent")
  • http://loinc.org#LA18198-4 ("No call")
  • http://loinc.org#LA11884-6 ("Indeterminate")

Answer options for /81251-1/81250-3/53034-5

  • http://loinc.org#LA6703-8 ("Heteroplasmic")
  • http://loinc.org#LA6704-6 ("Homoplasmic")
  • http://loinc.org#LA6705-3 ("Homozygous")
  • http://loinc.org#LA6706-1 ("Heterozygous")
  • http://loinc.org#LA6707-9 ("Hemizygous")

Answer options for /81251-1/81250-3/82120-7

  • http://loinc.org#LA26814-6 ("1st set of variants in cis relation to each other")
  • http://loinc.org#LA26815-3 ("2nd set of variants in cis relation to each other")
  • http://loinc.org#LA26816-1 ("3rd set of variants in cis relation to each other")
  • http://loinc.org#LA26817-9 ("4th set of variants in cis relation to each other")
  • http://loinc.org#LA26818-7 ("5th set of variants in cis relation to each other")
  • http://loinc.org#LA26320-4 ("Maternal")
  • http://loinc.org#LA26321-2 ("Paternal")
  • http://loinc.org#LA4489-6 ("Unknown")
  • http://loinc.org#LA46-8 ("Other")

Answer options for /81251-1/81250-3/82309-6

  • http://loinc.org#LA26426-9 ("Directly measured")
  • http://loinc.org#LA26427-7 ("Family DNA")
  • http://loinc.org#LA26428-5 ("Family history")
  • http://loinc.org#LA26429-3 ("Inferred from population data")

Answer options for /82118-1/53040-2

  • http://loinc.org#LA10315-2 ("Ultrarapid metabolizer")
  • http://loinc.org#LA25390-8 ("Rapid metabolizer")
  • http://loinc.org#LA25391-6 ("Normal metabolizer")
  • http://loinc.org#LA10317-8 ("Intermediate metabolizer")
  • http://loinc.org#LA9657-3 ("Poor metabolizer")

Answer options for /82118-1/51961-1

  • http://loinc.org#LA6676-6 ("Resistant")
  • http://loinc.org#LA6677-4 ("Responsive")
  • http://loinc.org#LA9660-7 ("Presumed resistant")
  • http://loinc.org#LA9661-5 ("Presumed responsive")
  • http://loinc.org#LA6682-4 ("Unknown Significance")
  • http://loinc.org#LA6675-8 ("Benign")
  • http://loinc.org#LA6674-1 ("Presumed Benign")
  • http://loinc.org#LA9662-3 ("Presumed non-responsive")

Answer options for /82118-1/83009-1

  • http://loinc.org#LA19542-2 ("Low risk")
  • http://loinc.org#LA19541-4 ("High risk")

Answer options for /82118-1/82117-3/82116-5

  • http://loinc.org#LA26421-0 ("Consider alternative medication")
  • http://loinc.org#LA26422-8 ("Decrease dose")
  • http://loinc.org#LA26423-6 ("Increase dose")
  • http://loinc.org#LA26424-4 ("Use caution")
  • http://loinc.org#LA26425-1 ("Normal response expected")

Answer options for /83011-7/81250-3/83005-9

  • http://loinc.org#LA26801-3 ("Simple variant")
  • http://loinc.org#LA26802-1 ("Structural variant")

Answer options for /83011-7/81250-3/48019-4

  • http://loinc.org#LA9658-1 ("Wild type")
  • http://loinc.org#LA6692-3 ("Deletion")
  • http://loinc.org#LA6686-5 ("Duplication")
  • http://loinc.org#LA6687-3 ("Insertion")
  • http://loinc.org#LA6688-1 ("Insertion/Deletion")
  • http://loinc.org#LA6689-9 ("Inversion")
  • http://loinc.org#LA6690-7 ("Substitution")
  • http://loinc.org#LA14033-7 ("Copy number gain")
  • http://loinc.org#LA14034-5 ("Copy number loss")
  • http://loinc.org#LA26324-6 ("Mobile element insertion")
  • http://loinc.org#LA26325-3 ("Novel sequence insertion")
  • http://loinc.org#LA26326-1 ("Tandem duplication")
  • http://loinc.org#LA26327-9 ("Intrachromosomal breakpoint")
  • http://loinc.org#LA26328-7 ("Interchromosomal breakpoint")
  • http://loinc.org#LA26331-1 ("Translocation")
  • http://loinc.org#LA26330-3 ("Complex")
  • http://loinc.org#LA26329-5 ("Sequence alteration")

Answer options for /83011-7/81250-3/48006-1

  • http://loinc.org#LA9658-1 ("Wild type")
  • http://loinc.org#LA6692-3 ("Deletion")
  • http://loinc.org#LA6686-5 ("Duplication")
  • http://loinc.org#LA6694-9 ("Frameshift")
  • http://loinc.org#LA6695-6 ("Initiating Methionine")
  • http://loinc.org#LA6687-3 ("Insertion")
  • http://loinc.org#LA9659-9 ("Insertion and Deletion")
  • http://loinc.org#LA6698-0 ("Missense")
  • http://loinc.org#LA6699-8 ("Nonsense")
  • http://loinc.org#LA6700-4 ("Silent")
  • http://loinc.org#LA6701-2 ("Stop Codon Mutation")

Answer options for /83011-7/81250-3/48002-0

  • http://loinc.org#LA6683-2 ("Germline")
  • http://loinc.org#LA6684-0 ("Somatic")
  • http://loinc.org#LA10429-1 ("Fetal")
  • http://loinc.org#LA18194-3 ("Likely germline")
  • http://loinc.org#LA18195-0 ("Likely somatic")
  • http://loinc.org#LA18196-8 ("Likely fetal")
  • http://loinc.org#LA18197-6 ("Unknown genomic origin")
  • http://loinc.org#LA26807-0 ("De novo")

Answer options for /83011-7/81250-3/81304-8

  • http://loinc.org#LA26398-0 ("Sequencing")
  • http://loinc.org#LA26399-8 ("Oligo aCGH")
  • http://loinc.org#LA26400-4 ("SNP array")
  • http://loinc.org#LA26401-2 ("BAC aCGH")
  • http://loinc.org#LA26402-0 ("Curated")
  • http://loinc.org#LA26403-8 ("Digital array")
  • http://loinc.org#LA26404-6 ("FISH")
  • http://loinc.org#LA26405-3 ("Gene expression array")
  • http://loinc.org#LA26406-1 ("Karyotyping")
  • http://loinc.org#LA26407-9 ("MAPH")
  • http://loinc.org#LA26408-7 ("MALDI-TOF")
  • http://loinc.org#LA26808-8 ("Merging")
  • http://loinc.org#LA26414-5 ("Multiple complete digestion")
  • http://loinc.org#LA26415-2 ("MLPA")
  • http://loinc.org#LA26417-8 ("Optical mapping")
  • http://loinc.org#LA26418-6 ("PCR")
  • http://loinc.org#LA26419-4 ("qPCR (real-time PCR)")
  • http://loinc.org#LA26420-2 ("ROMA")
  • http://loinc.org#LA26809-6 ("Denaturing high-pressure liquid chromatography (DHPLC)")
  • http://loinc.org#LA26810-4 ("DNA hybridization")
  • http://loinc.org#LA26811-2 ("Computational analysis")
  • http://loinc.org#LA26812-0 ("Single-stranded conformational polymorphism (SSCP)")
  • http://loinc.org#LA26813-8 ("Restriction fragment length polymorphism (RFLP)")

Answer options for /83011-7/81250-3/53037-8

  • http://loinc.org#LA6668-3 ("Pathogenic")
  • http://loinc.org#LA26332-9 ("Likely pathogenic")
  • http://loinc.org#LA26333-7 ("Uncertain significance")
  • http://loinc.org#LA26334-5 ("Likely benign")
  • http://loinc.org#LA6675-8 ("Benign")

Answer options for /83011-7/81250-3/69548-6

  • http://loinc.org#LA9633-4 ("Present")
  • http://loinc.org#LA9634-2 ("Absent")
  • http://loinc.org#LA18198-4 ("No call")
  • http://loinc.org#LA11884-6 ("Indeterminate")

Answer options for /83011-7/81250-3/53034-5

  • http://loinc.org#LA6703-8 ("Heteroplasmic")
  • http://loinc.org#LA6704-6 ("Homoplasmic")
  • http://loinc.org#LA6705-3 ("Homozygous")
  • http://loinc.org#LA6706-1 ("Heterozygous")
  • http://loinc.org#LA6707-9 ("Hemizygous")

Answer options for /83011-7/81250-3/82120-7

  • http://loinc.org#LA26814-6 ("1st set of variants in cis relation to each other")
  • http://loinc.org#LA26815-3 ("2nd set of variants in cis relation to each other")
  • http://loinc.org#LA26816-1 ("3rd set of variants in cis relation to each other")
  • http://loinc.org#LA26817-9 ("4th set of variants in cis relation to each other")
  • http://loinc.org#LA26818-7 ("5th set of variants in cis relation to each other")
  • http://loinc.org#LA26320-4 ("Maternal")
  • http://loinc.org#LA26321-2 ("Paternal")
  • http://loinc.org#LA4489-6 ("Unknown")
  • http://loinc.org#LA46-8 ("Other")

Answer options for /83011-7/81250-3/82309-6

  • http://loinc.org#LA26426-9 ("Directly measured")
  • http://loinc.org#LA26427-7 ("Family DNA")
  • http://loinc.org#LA26428-5 ("Family history")
  • http://loinc.org#LA26429-3 ("Inferred from population data")