Table. 1.

Examples of clinically-significant benign or likely benign COSMIC variants

Chr Start End Ref Alt Gene NT AA COSMIC dbSNP ClinVar HGMD GWAS catalog CIViC
11 69462910 69462910 G A CCND1 c.723G>A p.P241 COSM1179751 rs9344 Risk factor DFP NA NA
11 108175462 108175462 G A ATM c.5557G>A p.D1853N COSM41596 rs1801516 B/LB DP Melanoma NA
12 111884608 111884608 T C SH2B3 c.784T>C p.W262R COSM4985153 rs3184504 NA DFP Type 1 diabetes, etc. Colorectal cancer, predisposing, supports (evidence B)
15 74336633 74336633 T C PML c.1933T>C p.F645L COSM3754465 rs5742915 NA DP Paget’s disease NA
17 7579472 7579472 G C TP53 c.215C>G p.P72R COSM250061 rs1042522 Drug response DFP NA Breast cancer, predisposing; cervical cancer, prognostic; lung carcinoma, prognostic; not supports (evidence B)
19 10469975 10469975 A C TYK2 c.2051T>G p.I684S COSM438469 rs12720356 B/LB DFP Crohn’s disease, psoriasis NA
19 10475652 10475652 C A TYK2 c.1084G>T p.V362F COSM3756274 rs2304256 B DP Type 1 diabetes NA
5 1280028 1280028 G A TERT c.1950+245C>T NA COSN14994608 rs2242652 B DFP Prostate cancer NA
5 1286516 1286516 C A TERT c.1574-3777G>T NA COSN17007490 rs2736100 Association DP Lung adenocarcinoma, etc. Glioma, predisposing, supports (evidence B)
5 35874575 35874575 C T IL7R c.731C>T p.T244I COSM132904 rs6897932 B DFP Multiple sclerosis NA
5 35876274 35876274 A G IL7R c.1066A>G p.I356V COSM5904807 rs3194051 B DFP Ulcerative colitis NA

Abbreviations: COSMIC, Catalog of Somatic Mutations in Cancer; Chr, chromosome; Ref, reference allele; Alt, alternative allele; NT, nucleotide; AA, amino acid; dbSNP, Single Nucleotide Polymorphism Database; HGMD, Human Gene Mutation Database; GWAS, genome-wide association study; CIViC, Clinical Interpretation of Variants in Cancer; DFP, disease-associated polymorphisms with supporting functional evidence; NA, not applicable; B, benign; LB, likely benign, disease-associated polymorphisms; DP, disease-associated polymorphisms.

Lab Med Qual Assur 2021;43:25~30 https://doi.org/10.15263/jlmqa.2021.43.1.25
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