Terminologies

Value Sets

This table contains a list of all the value sets defined as part of the Variant Pathogenicity Interpretation specification. Some of these value sets include concepts defined elsewhere, some contain their own inline identifier system definitions, and some do both.

Name	IRI	Description	Source
Value Set Extensibility Value Set	SEPIO:0000363	Whether or not a ValueSet can be extended by users	LOINC SEPIO-CG
Molecular Consequence Value Set	SEPIO:0000380	A classification of a genomic variant based on its effect on a transcript or its location with respect to the transcript.	SO
Clinical Significance Value Set	SEPIO:0000371	The role that a variant plays in the causing a genetic condition (see LOINC answer list https://r.details.loinc.org/AnswerList/LL4034-6.html)	LOINC
Region Annotation Value Set	SEPIO:0000343	A label applied to a sequence region	SO SEPIO
Allelic Phase Value Set	SEPIO:0000344	Value denoting whether sequence features lie on the same or different molecules	GENO
Allelic State Value Set	SEPIO:0000338	Describes the existence of an allele across multiple copies of a chromosome (Informed by LOINC answer list https://r.details.loinc.org/AnswerList/LL381-5.html but with additional codes for somatic mosaicism and asserted absence.)	GENO
Inheritance Pattern Value Set	SEPIO:0000416	Classifies the transmission pattern of a condition in a pedigree. (see LOINC Answer List https://r.details.loinc.org/AnswerList/LL3731-8.html)	HP GENO
Condition Mechanism Value Set	SEPIO-CG:65108	The particular type of allele that can lead to a condition	SO
In Silico Prediction Method Value Set	SEPIO:0000345	The type of InSilico Predictor	SEPIO
Criterion Assessment Outcome Value Set	SEPIO:0000347	Denotes whether the collected evidence is sufficient to meet a specified criteria or not	SEPIO
Allele Functional Assay Value Set	SEPIO:0000382	The functional measurement carried out in a given assay	OBI
Population Value Set	SEPIO-CG:65112	Label for a group of individuals with a shared genetic background	NCIT
Benign Missense Variation Rate Outcome Value Set	SEPIO:0000349	The rate of missense variation in a transcript that do not lead to a genetic condition	SEPIO
Condition Penetrance Value Set	SEPIO-CG:65114	The chance of having a particular genetic condition given the presence of a particular variant or damaged gene	HP
Condition Mechanism Strength Value Set	SEPIO:0000354	The strength of association between a genetic mechanism and a condition	SEPIO
ACMG Evidence Strength Value Set	SEPIO:0000353	Degree of support that a set of evidence lends to a subsequent statement	SEPIO
Disease Value Set	SEPIO:0000372	An alteration of health status resulting from a physiopathological mechanism, and having a homogeneous clinical presentation and evolution and homogeneous therapeutic possibilities. (From MONDO)	OMIM Orphanet DOID MeSH MONDO UMLS
Phenotype Value Set	SEPIO:0000375	The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment. (From NCIT)	HP
Reference Sequence Value Set	SEPIO-CG:65119	Any public, immutable, accessioned DNA, RNA or amino acid sequences.	REFSEQ ENSEMBL
Contributory Role Value Set	SEPIO-CG:65120	The role played by an agent in the creation of an artifact	SEPIO
Allele Origin Value Set	SEPIO:0000392	The source of an allele in an individual	GENO
Ascertainment Method Value Set	SEPIO:0000409	The method by which a set of people was chosen to define a group	SEPIO
Locus Specificity Value Set	SEPIO:0000348	The degree to which a condition implicates a specific genomic locus, such as a gene.	SEPIO SEPIO-CG
Allele Conservation Value Set	SEPIO-CG:65124	The degree to which an allele is preserved over evolutionary history	SEPIO-CG
Parental Confirmation Value Set	SEPIO-CG:65125	Whether or not parentage has been confirmed with a genetic test	SEPIO-CG
Condition Status Value Set	SEPIO-CG:65126	Whether or not an individual is affected by a specific genetic condition	SEPIO-CG
Inconsistent Segregation Observed Value Set	SEPIO-CG:65127	Whether or not inconsistent segretations have been observed in a pedigree	SEPIO-CG
Null Allele Outcome Value Set	SEPIO-CG:65128	Denotes whether an allele leads to a non-functional transcript	SO
Region Alleles Outcome Value Set	SEPIO-CG:65129	Whether or not an allele overlaps a sequence region	SEPIO-CG
Gene Value Set	SEPIO:0000396	The genes in the the genome.	HGNC NCBIGene
ACMG Criterion Value Set	SEPIO:0000395	The ACMG-AMP IVS variant pathogenicity rule or criterion codes including extended codes used in domain specific derivatives of the original guideline. (e.g. BA1, PS2, PM3, PVS1, ...)	SEPIO-CG
Variant Interpretation Guideline Value Set	SEPIO-CG:65132	The assertion method guidelines for variant pathogenicity interpretation. ACMG-AMP IVS guidelines 2015 is a typical case, but there may be alternative or derivative guidelines as well.	SEPIO-CG
Variant Interpretation Criterion Scoring Rules Value Set	SEPIO-CG:65133	This is the description of how the weighting of the satisfied criterion are typically evaluated to arrive at a specific clinical significance.	SEPIO-CG
Inconsistent Segregation Status Value Set	SEPIO-CG:65140	TODO	SEPIO
Placeholder Empty Value Set	SEPIO-CG:65900	TODO	SEPIO-CG
Canonical Allele Type Value Set	SEPIO-CG:65901	TODO	SEPIO-CG
Allele Complexity Value Set	SEPIO-CG:65902	TODO	SEPIO-CG
Allele Name Type Value Set	SEPIO-CG:65903	TODO	SEPIO-CG
Contextual Allele Type Value Set	SEPIO-CG:65904	TODO	SEPIO-CG
Chromosome Value Set	SEPIO-CG:65905	TODO	SEPIO-CG
Reference Genome Build Value Set	SEPIO-CG:65906	TODO	SEPIO-CG