1: CODING # Coding System name HL7 V2 Linkage Name HL7 OID Description and sources 1 Cytogenetic location 2.16.840.1.113883.6.335 Source Organization: National Center for Biotechnology Information (NCBI) Source table information: Pending Source table download: Pending Place to Explore Table : https://lforms-service.nlm.nih.gov/apidoc/cytogenetic_locs/v1/doc.html Description: Chromosome location (AKA chromosome or cytogenetic location), is the standardized syntax for recording the position of genes and large mutations. It consists of three parts: the Chromosome number (e.g. 1-22, X, Y), an indicator of which arm – either “p” for the short or “q” for the long, and then a series of numbers separated by dots that indicate the band, sub band and sub-sub band of the locus (e.g. 2p16.3). There are other conventions for reporting ranges and locations at the ends of the chromosomes. The of these chromosome locations was loaded with all of the locations found in NCBI’s ClinVar variation tables. It will expand as additional sources become available. This does not include all finely grained chromosome locations that exist. Users can add to it as needed. We have not found a table of chromosome locations with standard codes. Balloters: if you know of a publicly available and maintained list of chromosome locations with standard codes please forward to us. Balloters: Adjacent chromosome locations are sometimes together (e.g. as “4q23.1q23.2”) or we have also seen them as “4q23.1-q23.2” which we think is clearer. Is one strongly preferred over the other?
Identifier and Codes (LOINC)® Source table download: http://loinc.org/downloads Place to Explore Table : https://lforms-service.nlm.nih.gov/apidoc/loinc/v1/doc.html Copyright: Regenstrief Institute, http://loinc.org/terms-of-use Description: Logical Observation Identifiers and Codes (LOINC®) provides a set of universal codes and names for identifying laboratory and other clinical observations. One of the main goals of LOINC is to facilitate the exchange and pooling of results for clinical care, outcomes management, and research. LOINC was initiated by Regenstrief Institute research scientists who continue to develop it with the collaboration of the LOINC Committee. 19 Locus Reference Genomic (LRG) 2.16.840.1.113883.6.337 Source organization: Locus Reference Genomic (LRG) Source table information: http://www.lrg-sequence.org/about Source table download: http://www.lrg-sequence.org/downloads Place to Explore Table : not implemented Description: LRG is a manually curated record that contains stable, and thus un-versioned, reference sequences designed specifically for reporting sequence variants with clinical implications. It provides a genomic DNA sequence representation of a single gene that is idealized, has a permanent ID (with no versioning), and core content that never changes. Their database includes maps to NCBI, Ensembl and UCSC reference sequences. It contained sequences for a total of 1073 genes as of April 2016, with identifiers of the form: "LRG_####", where #### can be from 1 to N, and N is the last gene processed. See PMIDs: 24285302, 20398331, and 20428090 for more information. RefSeq
C.6 NM Genomic structural variant copy number 3.1 1 O 0..1 The copy number of the large variant when applicable. In HGVS, this is the numeric value following the “X”. It is a unit-less value. Note that a copy number of 1 implies a deletion. The copy number can usually be inferred from the HGVS or ISCN fields. C.7 NR 81287-5 Genomic structural variant start-end 3.1 14184616^15581544 O 0..1 The reported start and end of the structural variant, when distinctions between outer bound and inner bounds are not made. A common reality. (See Rows G and Row H). C.8 NM 81299-0 Genomic structural variant reported arrCGH ratio 3.1 .48 C 0..1 Usually only applicable to ArrCGH and related studies. Its value is a number less than 1. C.9 CWE 81289-1 DNA structural variation type 3.1 LA6686-5^Deletion^LN O 0..1 Answer List: LL4033-8 Answer list is taken from the NCBI dbVar website which was taken from Sequence Ontology . The DNA structural variation type is also often carried in the HGVS expression, but as a shortened abbreviation.