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.

RESTful for direct linking to specific variant

If you want to put systematic URL links on your allele registry for each variant with one click
Here are the methods:
1. Assumed your variant is located in chromosome 1, the coordinate is 115256529,build as hg19, the reference allele is T , the alternative allele is C,
then the systematic URL link will be:
"http://cancervar.wglab.org/results_new_pos.php?queryType=position&build=hg19&chr=1&pos=115256529&ref=T&alt=C ", click to test
This URL will bring you to the "Re-Interpret" page directly, also with all automated criteria.

2.Or use link to get the json file:
"http://cancervar.wglab.org/api_new.php?queryType=position&build=hg19&chr=1&pos=115256529&ref=T&alt=C", click to test


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)
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