NTR: interpretation of clinical variant

[Dalalghamdi]

interpretation of clinical variant protocol Label: interpretation of clinical variant protocol Definition: a protocol that describes the process of assigning a formal classification of the clinical significance of the sequence change. Definition source: derived from PMID: 25741868 Parent class:

interpretation of clinical variant assay Label: clinical variant interpretation assay Alternative term(s): variant clinical impact classification Definition: An assay that assigns a formal classification of the clinical significance of the sequence change. Definition source: derived from PMID: 25741868 Parent class: assay (OBI_0000070) SubClass of: executes some 'interpretation of clinical variant protocol'

Clinical variant interpretation Label: Clinical variant interpretation Alternative term(s): clinical variant impact Definition: A data item representing a variant’s significance in relation to a disease or phenotype. Definition source: derived from PMID: 24033266 Parent class: data item (IAO_0000027)

benign variant Label: benign variant Definition: a clinical variant interpretation that represents a sequence variant previously classified or reported as a recognized neutral variant Definition source: inferred from College of American Pathologists (CAP) requirements Parent class: Clinical variant interpretation

likely benign variant Label: likely benign variant Definition: a clinical variant interpretation that represents a sequence variant that is previously unreported and is probably not causative of disease Definition source: inferred from College of American Pathologists (CAP) requirements Parent class: Clinical variant interpretation

likely pathogenic variant Label: likely pathogenic variant Definition: a clinical variant interpretation that represents a sequence variant that is previously unreported and is of the type which is expected to cause the disorder. Definition source: inferred from College of American Pathologists (CAP) requirements Parent class: Clinical variant interpretation

pathogenic variant Label: pathogenic variant Definition: a clinical variant interpretation that represents a sequence variant that is previously reported and is a recognized cause of the disorder. Definition source: inferred from College of American Pathologists (CAP) requirements Parent class: Clinical variant interpretation

variant of unknown significance Label: variant of unknown significance Definition: a clinical variant interpretation that represents a sequence variant that is previously unreported and is of the type which may or may not be causative of the disorder. Definition source: inferred from College of American Pathologists (CAP) requirements Parent class: Clinical variant interpretation

[cstoeckert]

Hi @Dalalghamdi I'm wondering whether "interpretation of clinical variant assay" is really an assay since the input is data (sequence change) as opposed to some material. If I got that right, what do you think about it being "drawing a conclusion based on data" OBI_0000338 instead?

[Dalalghamdi]

Hi @cstoeckert thank you for the clarification, yes I agree with you, I think it should be as a subclass of "drawing a conclusion based on data"

[DanBerrios]

Discussed on OBI call 4/11/22. OBI proposes:

Clinical variant interpretation Label: Clinical variant interpretation Alternative term(s): clinical variant impact Definition: A conclusion based on data representing a variant’s significance in relation to a disease or phenotype. Definition source: derived from PMID: 24033266 Parent class: Conclusion based on data

[DanBerrios]

Clinical variant interpretation assay Label: Clinical variant interpretation Alternative term(s): clinical variant impact Definition: The drawing of a conclusion regarding a variant’s significance in relation to a disease or phenotype. Definition source: derived from PMID: 24033266 Parent class: drawing a conclusion based on data http://purl.obolibrary.org/obo/OBI_0000338 has_specified_output: Conclusion based on data

[DanBerrios]

@Dalalghamdi Please review the proposed term attributes above, and let us know if you agree.

[Dalalghamdi]

@DanBerrios Thanks Dan, Yes I agree.

[cstoeckert]

@Dalalghamdi @ddooley discussed on OBI June 6, 2022 call. Please go ahead and make a PR for these. We can take another look to review at that time.