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Table 3 Activating mutations detected and MSI status in the studied population

From: Targeted next generation sequencing provides insight for the genetic alterations in liquid biopsy of Egyptian brain tumor patients

Gene Variant Substitution dbSNP ID HGVSc HGVSp Number of cases In silico predictions FATHMM prediction ClinVar COSMIC ID MSI result (number of cases)
Sift PolyPhen
KIT A > C Missense rs3822214 c.1621A > C p.(Met541Leu) 2 Tolerated (0.37) Benign (0.005) Pathogenic (score 0.74) Benign/likely benign COSM28026 MSI -L (2)
TP53 C > G Missense rs1042522 c.215C > G p.(Pro72Arg) 6 Tolerated (0.57) Benign (0.045) Neutral (score 0.36) Drug response COSM250061
COSM3766191
MSI -L (3)
MSI- H (3)
KDR A > T Missense rs1870377 c.1416A > T p.(Gln472His) 4 Tolerated (0.16) Benign (0.01) Neutral (score 0.07) Not recorded COSM149673 MSI -L (3)
MSI -H (1)
G > A Intron rs7692791 c.798 + 54G > A   6     Not recorded COSN8870412
COSN8870413
MSI -L (3)
MSI -H (3)
INDEL Intron rs869246746
rs3214870
rs397772062
c.2615-37dupC   4     Not recorded COSN17154192 MSI -L (3)
MSI -H (1)
JAK3 G > C Missense rs146837396 c.2152G > C p.(Val718Leu) 1 Deleterious (0.03) Benign (0.025) Pathogenic (score 0.80) Conflicting interpretations of pathogenicity;
Likely benign; uncertain significance
COSM5946070 MSI -H (1)
IDH1 C > T Coding silent rs11554137 c.315C > T p.(Gly105=) 1    Pathogenic (score 0.85) Benign COSM1741220 MSI-H (1)
APC G > A Coding silent rs41115 c.4479G > A p.(Thr1493=) 4    Neutral (score 0.46) Benign COSM3760869 MSI-L (2)
MSI -H (2)
EGFR G > A Coding silent rs1050171 c.2361G > A p.(Gln787=) 6    Pathogenic (score 0.95) Benign COSM1451600 MSI -L (3)
MSI -H (3)
CDKN2A A > C Coding silent rs201208890 c.174A > C p.(Arg58 =) 1     Benign/likely benign COSM6495276
COSM6495277
MSI -L
(1)
MET C > T Coding silent rs28444388 c.1131C > T p.(Ile377=) 1    Neutral (score 0.29) Benign COSM5020205 MSI -H (1)
C > T Coding silent rs35775721 c.534C > T p.(Ser178 =) 2    Not applicable Benign COSM1579024 MSI -L (1)
MSI -H (1)
PDGFRA C > T Coding silent rs2228230 c.2472C > T p.(Val824=) 3    Pathogenic (score 0.88) Benign COSM22413 MSI -L (2)
MSI -H (1)
A > G Coding silent rs1873778 c.1701A > G p.(Pro567=) 7    Neutral (score 0.02) Benign COSM7410554 MSI -L (4)
MSI -H (3)
RET C > G Coding silent rs1800863 c.2712C > G p.(Ser904=) 4    Neutral (score 0.27) Benign COSM3751779
COSM3751780
MSI -L (2)
MSI -H (2)
G > T Coding silent rs1800861 c.2307G > T p.(Leu769=) 7    Pathogenic (score 0.79) Benign COSM4418405
COSM4418406
MSI -L (4)
MSI -H (3)
HRAS T > C Coding silent rs12628 c.81T > C p.(His27 =) 2    Neutral (score 0.07) Benign COSM249860
COSM3752426
MSI -L (2)
FGFR3 G > A Coding silent rs7688609 c.1959G > A p.(Thr653 =) 7    Pathogenic (score 0.70) Not recorded COSM7410552 MSI -L (4)
MSI -H (3)
FLT3 T > C Intronic rs2491231 c.1310-3T > C   5    Neutral (score 0.02) Not recorded COSM3999060 MSI -L (2)
MSI -H (3)
SMARCB1 G > A Intronic rs5030613 c.1119-41G > A   2    Neutral (score 0.03) Benign COSM1090
COSN17135779
MSI -L (2)
PIK3CA A > G Intron rs3729674 c.352 + 40A > G   5     Uncertain significance COSN26959779
COSN26959780
MSI -L (3)
MSI -H (2)
STK11 T > C Intron rs2075606 c.465-51T > C   3     Uncertain significance COSN6666958 MSI -L (2)
MSI -H (1)
ERBB4 A > G Intron rs839541 c.421 + 58A > G   4     Not recorded COSN19690034
COSN27007111
MSI -L (1) MSI -H (3)
INDEL Splice region
Intron
rs67894136
rs397987661
c.884-7delT   7     Not recorded   MSI -L (4) MSI -H (3)
INDEL Splice region
Intron
rs748883732 c.884-8_884-7delTT   2     Not recorded   MSI -L (1)
MSI -H (1)
NPM1 INDEL Intron rs397792554
rs34323200
c.847-5delT   7     Not recorded   MSI -L (4)
MSI -H (3)
CSF1R MNV 3-prime UTR rs386693509 c.*35_*36delCAinsTC   7     Uncertain significance   MSI -L (4)
MSI -H (3)