Stepwise Vairant Classification and Interpretation

Copyrighted Figure, displaying here for educational purpose only. See reference below.
Reference: Horak P, et al. Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of ClinGen, CGC, and VICC. Genetics in Medicine 2022;24(5):986-998. (PMID: 35101336)

My presentation at CAPA 8th Diagnostic Course (9/10/2022)

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Click a link to visit the public database site

Is this variant oncogenic?

Classification of Variants Based on Oncogenicity Calculator js-html written by Dr. Thomas Schneider, Emory Pathology

Gnomad: Population database (not always germline)

The gnomad database is not user-friendly. You will need to figure out the specific format (see the Examples on the webpage) to perform a search. Or you can go to Varsome first and get the variant fromat from there.

Cancer Hotspot: Somatic mutations associated with cancer

VarSome: the human genomic variant search engine

How often do we see this variant in malignancies?
How often do we see this variant in the tested tumor type?

COSMIC: Catalogue of Somatic Mutation In Cancer

My Cancer Genome®: Genetically Informed Cancer Medicine

TCGA (The Cancer Genome Atlas): Harmonized Cancer Datasets

cBioPortal Public Site

cBioPortal Genie (larger database, need registration)

Watch the video demonstration

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Evidence-based variant categorization

Copyrighted Figure, displaying here for educational purpose only. See reference below.
Reference: Li, M. et al. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 2017;19(1):4-23. PMID: 27993330

OncoKB: MSK's Precision Oncology Knowledge Base

CKBBoost: The Clinical Knowledgebase, Powered by The Jackson Laboratory

CIVIC: Clinical Interpretation of Variants in Cancer

Stepwise Vairant Classification and Interpretation

My presentation at CAPA 8th Diagnostic Course (9/10/2022)

Click a link to visit the public database site

Is this variant oncogenic?

How often do we see this variant in malignancies? How often do we see this variant in the tested tumor type?

Watch the video demonstration

Evidence-based variant categorization

Watch the video demonstration

How often do we see this variant in malignancies?
How often do we see this variant in the tested tumor type?