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. 2020 Sep 22;147(1):117–128. doi: 10.1007/s00432-020-03391-8

Table 3.

Pathogenic SNPsa associated with the revised Bethesda guide line and extended in the training cohort

Itemsa Gene SNP ID Position: nucleotide change Predicted
AA change		 Genotype: control vs case, RR/RS/SS p-value MAF Clinical relevance PP-2/SIFT/ClinVar
Current Globalb
1 MUC16 rs112439001 NM_024690.2:c.40730G > A p.Ser13577Asn 59/11/0 vs 12/13/0 0.0009127 0.126 0.0455 NA/D/NA
2 SH2D4A rs35647122 NM_001174159.1:c.626A > G p.Glu209Gly 69/14/0 vs 0/3/0 0.0008036 0.198 0.0359 D/D/NA
2 OR5A2 rs17153691 NM_001001954.1:c.307 T > C p.Phe103Leu 77/14/0 vs 0/3/0 0.0003774 0.181 0.0449 D/T/NA
2 MMP27 rs2509010 NM_022122.2:c.1339G > A p.Asp447Asn 81/12/1 vs 1/1/1 0.0002847 0.155 0.1637 D/NA/NA
2 KRT76 rs2280480 NM_015848.4:c.1886C > T p.Thr629Met 68/20/3 vs 0/1/2 7.311e-06 0.277 0.1659 D/D/NA
2 DLGAP5 rs8010791 NM_014750.4:c.972A > C p.Gln324His 82/8/0 vs 1/1/1 3.261e-06 0.108 0.1176 D/D/NA
2 KAZN rs12048768 NM_201628.2:c.2287C > T p.Arg763Cys 68/11/1 vs 1/1/1 0.0006443 0.096 0.0513 NA/D/NA
2 ELMO3 rs79736950 NM_024712.3:c.1084C > T p.Arg362Trp 73/7/1 vs 0/3/0 3.315e-05 0.071 0.0118 NA/D/NA
2 CENPT rs11558533 NM_025082.3:c.364A > G p.Arg122Gly 66/15/1 vs 0/2/1 3.846e-05 0.124 0.0258 NA/D/NA
3 TAS2R4 rs2234000 NM_016944.1:c.221C > T p.Thr74Met 78/8/1 vs 5/4/1 0.0001884 0.144 0.0068 D/NA/NA
4 WARS2 rs3790549 NM_201263.2:c.165G > C p.Ala267Pro 71/15/1 vs 3/6/1 0.0001327 0.237 0.0968 D/NA/NA
4 KRTAP27-1 rs2244485 NM_001077711.1:c.296C > T p.Ala99Val 64/21/1 vs 2/6/1 0.0006876 0.305 0.3213 D/NA/NA
4 SIGLEC12 rs74354979 NM_053003.2:c.229G > A p.Ala77Thr 71/9/0 vs 5/3/1 0.0009324 0.079 0.096 NA/D/NA
5 ERICH3 rs2305549 NM_001002912.4:c.2072A > G p.His691Arg 67/21/3 vs 1/3/2 0.0001236 0.316 0.1176 D/NA/NA
5 ZNF366 rs13188519 NM_152625.2:c.2216C > G p.Ala739Glu 78/7/0 vs 3/1/1 0.0005157 0.1 0.0725 D/NA/NA
5 CCDC122 rs9567280 NM_144974.4:c.806 T > C p.Ile269Thr, 77/9/1 vs 3/2/1 0.0008882 0.14 0.0619 D/D/NA
5 GOLGB1 rs35674179 NM_004487.4:c.5138G > T p.Cys1718Phe 84/6/0 vs 3/2/1 5.938e-06 0.052 0.1218 NA/D/NA
7 THSD7A rs2285744 NM_015204.2:c.2313C > G p.Asp771Glu 60/16/0 vs 1/10/2 7.679e-05 0.169 0.721 D/D/NA
7 CTBP2 rs146419230 NM_022802.2:c.2897C > G p.Ala966Gly 65/11/0 vs 3/7/0 1.370 e-04 0.105 0.9999 NA/D/NA
7 MS4A14 rs7131283 NM_032597.4:c.529A > T p.Asn177Tyr 27/42/14 vs 1/4/8 0.0009599 0.468 0.6493 D/D/NA
8 FSCN3 rs3779536 NM_020369.2:c.70G > T p.Ala24Ser 62/9/0 vs 10/7/1 0.0009094 0.191 0.1106 D/D/NA
9 CCDC122 rs9567280 NM_144974.4:c.806 T > C p.Ile269Thr, 67/7/0 vs 13/4 2 0.0009795 0.14 0.0619 D/D/NA
9 NUP160 rs3816605 NM_015231.2:c.1051A > G p.Thr351Ala 26/36/12 vs 16/3/1 0.0009383 0.346 0.3458 NA/D/NA
10 THSD7A rs2285744 NM_015204.2:c.2313C > G p.Asp771Glu 60/16/0 vs 6/10/2 7.679e-05 0.1456 0.2788 D/D/NA
12 ANKK1 rs7118900 NM_178510.1:c.715G > A p.Ala239Thr 6/13/10 vs 25/22/3 0.000323 0.386 0.2533 NA/D/NA

SNP single nucleotide polymorphism, AA amino acid, SS two substitution alleles, SR one reference and one substitution alleles, RR two reference alleles, MAF minor allele frequency, D damaging in the PP-2 and deleterious in the SIFT, respectively, NA not available, CRC family history of colorectal cancer, GC family history of gastric cancer, DMMR deficiency in mismatch repair genes

aAll items are precisely defined in the Supplementary Table S1

bGlobal allele frequency according to the dbSNP provided by the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/snp/)

cPossible to probable pathogenic SNPs based on the PolyPhen-2 (Polymorphism Phenotyping v2; https://genetics.bwh.harvard.edu/pph2/), SIFT (Sorting Intolerant from tolerant; https://sift.bii.a-star.edu.sg/) and ClinVar (https://www.clinicalgenome.org/). Any of these three tools suggesting benign or likely benign were excluded from the clinical significance