Table 3 The 11 candidate SNPs showing significant frequencies differences between the different evaluated populations
From: Genetic susceptibility of bladder cancer in the Lebanese population
Groups | Types of SNPs | Type of amino acid change | Variants | Genes | A= Frequency in the studied Lebanese cohort | B= Frequency in the local Lebanese database | C= Frequency in gnomAD | Difference A vs. B | Difference A vs. C | 99.9999999% CI of A |
|---|---|---|---|---|---|---|---|---|---|---|
Group 1 | 3 Prime UTR Variant | Pyrimidine to pyrimidine | rs1707 | HLA-G | 0.529411765 | 0.20127119 | 0.8574 | Yes | Yes | [0.24714813–0.798697334] |
3 Prime UTR Variant | Pyrimidine to purine | rs1063320 | HLA-G | 0.215686275 | 0.0286017 | 0.516 | Yes | Yes | [0.04591686–0.509931283] | |
Group 2 | 3 Prime UTR Variant | Pyrimidine to pyrimidine | rs9299 | HOXB-AS3 | 0.12745098 | 0.19597458 | 0.531 | No | Yes | [0.01361905–0.402416044] |
3 Prime UTR Variant | Pyrimidine to pyrimidine | rs696 | NFKBIA | 0.019607843 | 0.14830509 | 0.4574 | No | Yes | [3.04E-06-0.227119758] | |
Non-Coding Transcript Variant | Purine to purine | rs1061217 | SLAMF1 | 0.509803922 | 0.28495763 | 0.00003191 | No | Yes | [0.23147854–0.783803061] | |
Intron Variant | Pyrimidine to pyrimidine | rs1799794 | XRCC3 | 0.009803922 | 0.00423729 | 0.2219 | No | Yes | [7.4861E-09-0.203334752] | |
Intron Variant | Pyrimidine to pyrimidine | rs1799796 | KLC1; XRCC3 | 0.205882353 | 0.194915254 | 0 | No | Yes | [0.04162045–0.49880505] | |
Intron Variant | Purine to purine | rs1805335 | RAD23B | 0.607843137 | 0.44809322 | 0.000004051 | No | Yes | [0.313778362–0.854357768] | |
Group 3 | 3 Prime UTR Variant | Purine to pyrimidine | rs1710 | HLA-G | 0.431372549 | 0.150423729 | 0.5169 | Yes | No | [0.172681469–0.720337798] |
Upstream gene_variant | Not applicable | rs3213239 | PINLYP | 0.411764706 | 0.13559322 | 0.6146 | Yes | No | [0.158961335–0.703483575] | |
Intron Variant | Purine to pyrimidine | rs1801320 | RAD51 | 0.019607843 | 0 | 0.1266 | Yes | No | [3.03998E-06-0.227119758] |