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

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)