Table 5 Unique pathogenic variants with (CScape score > 0.5) unique pathogenic variants in SMGs TCGA HCC and Non-HCC

chr17

7,578,508

Tier1

101.81

TP53

missense

c.422G > A

p.Cys141Tyr

LT19_HCC

0.9312

chr5

1,293,625

Tier3

8.8584

TERT

stop_gained

c.1376G > A

p.Trp459Ter

LT08_HCC

0.9082

chr8

103,855,852

Tier3

30.607

AZIN1

missense

c.29A > G

p.Tyr10Cys

LT14_HCC

0.8998

chr19

10,600,008

Tier3

10.393

KEAP1

missense

c.1568G > A

p.Gly523Glu

LT07_HCC

0.8945

chr3

52,437,608

Tier3

6.2349

BAP1

missense

c.1553G > A

p.Arg518Gln

LT07_HCC

0.8922

chr3

178,952,085

Tier1

6.2381

PIK3CA

missense

c.3140A > G

p.His1047Arg

LT10_HCC

0.8043

chr8

103,845,284

Tier3

6.7846

AZIN1

missense

c.904G > A

p.Val302Ile

LT11_HCC

0.7754

chr2

21,227,996

Tier3

205.82

APOB

missense

c.11744C > T

p.Ser3915Phe

LT19_HCC

0.7374

chr1

27,100,124

Tier3

6.2383

ARID1A

missense

c.3920C > T

p.Pro1307Leu

LT07_HCC

0.6783

chr9

21,974,732

Tier2

25.112

CDKN2A

missense

c.95 T > A

p.Leu32Gln

LT14_HCC

0.5713

chr1

27,094,369

Tier3

4.1526

ARID1A

missense

c.3077G > A

p.Arg1026His

LT07_Non

0.9154

chr16

354,405

Tier3

11.843

AXIN1

missense

c.1153C > T

p.Pro385Ser

LT07_Non

0.879

chr3

52,442,605

Tier2

5.7804

BAP1

frameshift

c.140_141insG

p.Ile47MetfsTer22

LT19_Non

0.856

chr3

52,442,545

Tier2

5.785

BAP1

frameshift

c.201dup

p.Asp68Ter

LT19_Non

0.85

chr2

178,098,885

Tier3

7.2747

NFE2L2

frameshift

c.160_161insA

p.Leu54HisfsTer2

LT10_Non

0.7653

chr16

348,239

Tier3

5.0519

AXIN1

frameshift

c.1267_1268insC

p.Glu423AlafsTer46

LT10_Non

0.6795

chr19

4,154,960

Tier3

5.8058

CREB3L3

missense

c.92A > G

p.Asp31Gly

LT10_Non

0.6625

chr2

21,239,431

Tier3

8.8517

APOB

missense

c.3212 T > C

p.Val1071Ala

LT18_Non

0.6298

chr2

21,229,673

Tier3

7.8123

APOB

missense

c.10067 T > C

p.Leu3356Pro

LT10_Non

0.588

chr8

10,465,934

Tier3

16.263

RP1L1

missense

c.5674A > G

p.Thr1892Ala

LT18_Non

0.5742