ABCDEFGHIJKLMNOPQRSTUVWXYZAA
1
CodeScopeDescription on http://build.fhir.org/ig/HL7/genomics-reporting/sequencing.htmlShort nameGlossary DefinitionenumerationSO branchNotes
2
DNA Change Type48019-4Annotation Component on Variant.may be required for certain types of structural variants. See below.coding-change-typeCodified type for associated DNA Marker. DNA Markers 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. Enumeration: Children of Sequence Ontology, SO:0002072DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072: deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)sequence_comparison "A position or feature where two sequences have been compared."Created concept map to Loinc: http://build.fhir.org/ig/HL7/genomics-reporting/ConceptMap-dna-change-type-map.html
3
4
Amino Acid Change Type48006-1Annotation Component on Variant.Amino Acid Change TypeCodified type for the protein (amino acid) sequence change, as implied by the pHGVS section of the variant's HGVS string.LOINC Answer List LL380-7 (extensible): Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | SilentRelated to polypeptide_sequence_variant but from the perspective of Sequence comparison...Used in mCODE
5
6
Molecular Consequencemolecular-consequenceAnnotation Component on Variantavailable from NCBI, tied to representative transcriptmolecular-consequenceA calculated classification of the effect of the gene's sequence change on the resulting amino acid (protein) sequence change, reported per transcript. Enumerated by the children of Sequence Ontology SO:0001537Concepts in sequence ontology under SO:0001537: stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)structural_variant "A sequence variant that changes one or more structural features."snpEff and Clinvar use some sequence_feature or sequence_alteration codes here too
7
8
Functional Effect
functional-effect
Diagnostic Implication Componentfunctional-effectA predicted or observed effect of a variant on its gene's (or protein product thereof) ability to function. Value set enumeration is to be the children of Sequence Ontology SO:0001536.gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect (extensible): Sequence Ontology terms under SO:0001536		functional_effect_variant "A variant whereby the effect is evaluated with respect to a reference."
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100