CancerVar: a web server for improved evidence-based clinical interpretation for cancer somatic mutations

CancerVar is a bioinformatics software tool for clinical interpretation of somatic variants by evidence from AMP/ASCO/CAP/CGC 2017-2019 guideline. The input to CancerVar can be genomic coordinate,dbSNP ID, gene with cDNA change, gene with Protein change, while the output of CancerVar is the interpretation of variants as clinical significance: 'Tier I/Pathogenic: Variants of Strong Clinical Significance','Tier II/Likely Pathogenic: Variants of Potential Clinical Significance','Tier III: Variants of Unknown Clinical Significance' and 'Tier IV: Benign or Likely Benign Variants', together with detailed evidence.


Please check/uncheck following criteria and select the weight for your variant:
(If you has the position of your missense/indel variant, you can clik here to search your variant.)

CBP1 Therapeutic: FDA approved or investigational with strong evidence
CBP2 Diagnostic: In Professional guideline or reported evidence with consensus
CBP3 Prognostic: In Professional guideline or reported evidence with consensus
CBP4 Mutation type: Activating, LOF (missense, nonsense, indel, splicing), CNVs, fusions
CBP5 Variant frequencies:Mostly mosaic
CBP6 Potential germline: Mostly nonmosaic
CBP7 Population database: Absent or extremely low MAF
CBP8 Germline database: may be present in HGMD/ClinVar as pathogenic
CBP9 Somatic database: Most likely present in COSMIC, My Cancer Genome, TCGA, ICGC
CBP10 Predictive Mostly damaging: SIFT, PolyPhen2,MutationAssessor,MetaSVM,MetaLR,FATHMM,GERP++_RS
CBP11 Pathway involvement: Disease-associated pathways or pathogenic pathways
CBP12 Publications: functional study, population study, other
CBP13 Additional: user specified

Weight: Strong: Grade 2;     Supporting: Grade 1;     No: Grade 0;     Negative/Benign: Grade -1;



Reference

1. Li MM, 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 Jan;19(1):4-23. doi: 10.1016/j.jmoldx.2016.10.002.
2.Mikhail FM, et al. Technical laboratory standards for interpretation and reporting of acquired copy-number abnormalities and copy-neutral loss of heterozygosity in neoplastic disorders: a joint consensus recommendation from the American College of Medical Genetics and Genomics (ACMG) and the Cancer Genomics Consortium (CGC). Genet Med. 2019 Sep;21(9):1903-1916. doi: 10.1038/s41436-019-0545-7.
3.Quan Li and Kai Wang. InterVar: Clinical interpretation of genetic variants by ACMG-AMP 2015 guideline(The American Journal of Human Genetics 100, 1-14, February 2, 2017,http://dx.doi.org/10.1016/j.ajhg.2017.01.004)