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Table 2 All selected variants

From: Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis

Participant

Gene symbol

Refseq

Nucleotide substitution

Predicted protein alteration

VAF (a)

cBioportal (b)

gnomAD

Variant interpretation

A

CHEK2

NM_001005735.1

1229delC (1100delC)

Thr410Metfs*15

0.4

Ab

0.008717

Risk factor

A

SDHA

NM_004168.2

1724C > T

Ala575Val

0.4

Bc

0.0001386

VUS

A

ABCB11

NM_003742

1724G > A

Arg575Gln

0.4

Bb

0.0003315

VUS

A

HOXB13

NM_006361

251G > A

Gly84Glu

0.5

Ac

0.007618

Risk factor

A

MLH1

NM_000249

27G > A

Arg9=

0.5

Ba

0

Likely pathogenic

B

CHEK2

NM_001005735.1

670C > T

Arg224Cys

0.7

Ab

0.0005227

VUS

B

KLLN

NM_001126049.1

422G > A

Thr141Met

0.6

C

0

VUS

B

REST

NM_005612

968 T > G

Met323Arg

0.5

Ac

0

VUS

B

TRIM28

NM_005762

2381C > T

Thr794Met

0.5

Ab

0.0001986

VUS

B

LZTR1 (c)

NM_006767

1866_1867delTC

Pro623ThrfsTer45

0.5

Bb

0

VUS

C

BAP1

NM_004656.3

944A > C

Glu315Ala

0.4

Bb

0.0003263

VUS

C

FBXW7

NM_001013415

248G > A

Arg83Lys

0.5

Bc

0.0005178

VUS

C

RMRP (c)

NR_003051

71A > G

NA

0.4

C

0.008687

Pathogenic incidental finding

C

SMO

NM_005631.4

517C > T

Arg173Cys

0.5

Bb

0.0007454

VUS

E

ARID1B

NM_020732.3

4727C > T

Pro1576Leu

0.4

Ac

0.00003098

VUS

E

MLH1

NM_000249.3

41C > T

Thr14Ile

0.7

Bc

0.000008792

VUS

E

SSX1

NM_005635

293dupA

Met99AspfsTer24

0.6

Bc

0.0002149

VUS

E

FAT4

NM_024582

7751C > A

Ser2584Tyr

0.5

Bc

0.00005789

VUS

E

TOP2A

NM_001067

154G > A

Gly52Ser

0.4

Bc

0

VUS

E

MEN1

NM_000244

654C > A

Ala213=

0.6

Bc

0

Likely pathogenic

F

TYR (c)

NM_000372.4

1147G > A

Asp383Asn

0.6

Ab

0.0001784

Pathogenic incidental finding

G

ERCC3 (c)

NM_000122.1

1204G > A

Gly402Ser

0.5

Bc

0.00004006

VUS

G

CTNNB1

NM_001098210.1

319A > G

Met107Val

0.5

Ac

0

VUS

G

TCF3

NM_003200

689C > G

Pro230Arg

0.5

Bc

0.00001430

VUS

H

RNF6

NM_005977

1780C > A

Leu594Ile

0.4

Bc

0

VUS

H

RNF6

NM_005977

895G > C

Glu299Gln

0.3

Bc

0.000008792

VUS

H

ARHGAP26

NM_015071

619C > G

Leu207Val

0.5

Bc

0.00001760

VUS

H

XRCC3

NM_005432

172C > T

Arg58Trp

0.5

Ac

0.00006208

VUS

H

TSC2

NM_000548

1244C > T

Ala415Val

0.5

Ac

0.0001866

VUS

J

TCF3

NM_003200

c.1213C > T

p.Arg405Cys

0.5

Ac

0.00008796

VUS

J

PNP (c)

NM_000270

c.701G > C

p.Arg234Pro

0.6

C

0.0001471

Pathogenic incidental finding

J

ARHGAP26

NM_015071

c.1559A > G

p.Gln520Arg

0.5

C

0.00006175

VUS

  1. VUS Variant of unknown significance
  2. (a) VAF; variant allele fraction (alternate/(reference + alternate))
  3. (b) cBioPortal [26]:
  4. A: Same variant
  5. B: Other similar variant in proximity
  6. C: No similar variant in proximity
  7. a: Same tumour types
  8. b: Overlapping tumour types
  9. c: Other tumour types
  10. (c) Gene associated to potentially cancer-associated syndrome described in OMIM (Online Inheritance in Man) [40] with a recessive inheritance pattern, including those with both recessive and dominant inheritance patterns