Table 1. PAVs classified as deleterious by CONDEL associated with glioma risk at P <10−3.
| All glioma Ncase/control=1882/8079 | GBM Ncase=771 | Non-GBM Ncase=928 | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| HGVS genomic | Allele frequency | |||||||||
| dbSNP rsid | Description | Gene | Case | Control | P | Odds ratio | P | Odds ratio | P | Odds ratio |
| rs185338080 | chr17:g.7329692C>T | C17orf74 | 0.00267 | 5.60 × 10−4 | 4.73 × 10−5 | 6.87 (2.71–18.4) | 7.35x10−6 | 12.3 (4.11–37.0) | 0.0374 | 4.29 (1.09–16.9) |
| rs200918780 | chr2:g.103340351G>C | MFSD9 | 0.00213 | 7.43 × 10−4 | 9.78 × 10−5 | 8.80 (2.95–26.3) | 0.00153 | 8.99 (2.31–34.9) | 0.00109 | 9.62 (2.47–37.4) |
| rs144793260 | chr5:g.52193318A>G | ITGA1 | 0.00133 | 3.09 × 10−4 | 1.08 × 10−4 | 25.6 (4.96–134) | 0.00241 | 20.9 (2.93–149) | 0.00193 | 22.4 (3.14–159) |
| rs200058353 | chr15:g.42983771C>G | KIAA1300 | 0.00133 | 1.86 × 10−4 | 1.08 × 10−4 | 25.6 (4.96–132) | 0.0560 | 10.4 (0.94–115) | 1.157 × 10−5 | 45.1 (8.22–247) |
| rs41281932 | chr9:g.100116970A>G | KIAA1529 | 0.00478 | 0.00173 | 1.22 × 10−4 | 3.48 (1.84–6.57) | 2.68 × 10−4 | 4.15 (1.93–8.92) | 0.0316 | 2.77 (1.09–7.02) |
| rs2229388 | chr8:g.16012648G>C | MSR1 | 0.0689 | 0.0545 | 1.25 × 10−4 | 1.36 (1.16–1.59) | 0.00144 | 1.41 (1.14–1.74) | 0.0304 | 1.26 (1.02–1.56) |
| rs140963213 | chr11:g.67814983G>A | TCIRG1 | 0.00956 | 0.00464 | 1.41 × 10−4 | 2.33 (1.51–3.60) | 0.0199 | 2.08 (1.12–3.87) | 5.52 × 10−4 | 2.62 (1.52–4.52) |
| rs147288996 | chr5:g.140057509C>T | HARS | 0.00452 | 0.00167 | 2.08 × 10−4 | 3.28 (1.75–6.15) | 2.83 × 10−4 | 3.93 (1.88–8.22) | 0.00105 | 5.45 (1.98–15.0) |
| rs78805068 | chr5:g.140308281C>T | PCDHAC1 | 0.00452 | 0.00161 | 2.14 × 10−4 | 3.38 (1.77–6.44) | 1.91 × 10−4 | 4.11 (1.96–8.65) | 0.00105 | 5.45 (1.98–15.0) |
| rs149397155 | chr3:g.15298590C>T | SH3BP5 | 0.00213 | 0.00124 | 5.47 × 10−4 | 4.33 (1.89–9.93) | 7.16 × 10−4 | 5.55 (2.06–15.0) | 0.253 | 2.35 (0.54–10.1) |
| rs118101777 | chr15:g.90630704C>T | IDH2 | 0.00425 | 0.00155 | 5.50 × 10−4 | 3.11 (1.63–5.91) | 0.00302 | 3.41 (1.52–7.67) | 0.00767 | 3.21 (1.36–7.57) |
| rs201460298 | chr7:g.111375137G>C | DOCK4 | 0.00159 | 1.86 × 10−4 | 6.60 × 10−4 | 12.4 (2.91–52.8) | 1.63 × 10−4 | 31.5 (5.24–189) | 0.0111 | 10.5 (1.71–64.8) |
| rs139894978 | chr7:g.156755735C>G | NOM1 | 0.00266 | 0.00192 | 8.00 × 10−4 | 3.43 (1.67–7.06) | 0.0551 | 2.80 (0.98–7.99) | 8.38 × 10−4 | 4.52 (1.87–11.0) |
| rs74720216 | chr17:g.8159165G>A | PFAS | 0.0122 | 0.0182 | 8.84 × 10−4 | 0.57 (0.40–0.79) | 0.0714 | 0.66 (0.42–1.04) | 0.0165 | 0.58 (0.37–0.91) |
| rs2822432 | chr21:g.15516948C>T | LIPI | 0.363 | 0.331 | 1.00 × 10−3 | 1.15 (1.06–1.25) | 0.0460 | 1.12 (1.00–1.26) | 0.00145 | 1.20 (1.07–1.34) |
P-values and odds ratios (ORs) estimated from fixed-effects meta-analysis of logistic regression beta values, assuming an additive model. Variants are ordered by glioma association P-value. HGVS, human genome variation society. ORs and allele frequencies derived with respect to underlined allele in HGVS genomic description. All genomic variant descriptions based on genome build hg19.