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Table 1 Variants with potential clinical significance. Putative somatic variants are identified as those with < 1% allele frequency in the 1000 genomes population and alternate allele frequency > 70% or < 30%, or those annotated in COSMIC

From: Somatic variants of potential clinical significance in the tumors of BRCA phenocopies

Case #
Variant in First Degree Relative
Genea,b Loc Variant Read Depth Variant Frequencyc Effect on Proteind Population Frequencye
1
BRCA2 c.C5645A
PDE4DIP chr1 c.4993_4995CG 1084 0.39 NA NA
FOXP1 chr3 c.C343G:p.P115A 487 0.26 0.996 0.0005
PIK3CA a chr3 c.A3140G:p.H1047R 654 0.28 0.639 NA
APC chr5 c.G7450A:p.G2484S 274 0.43 0.234 0.01
SMO chr7 c.C1939T:p.P647S 65 0.72 1 0.0032
CNTRL chr9 c.G5809A:p.E1937K 349 0.44 0.841 0.0018
TET1 chr10 c.C767T:p.A256V 414 0.58 0.022 0.1
ZMYM2 chr13 c.G454C:p.D152H 441 0.28 0.997 0.0023
ZMYM5 chr13 c.A691G:p.T231A 105 0.21 0.014 0.09
MTUS2 chr13 c.C2870T:p.T957 M 461 0.27 0.062 0.02
2
BRCA1c.IVS17 + 3 A > G
EPHA10 chr1 c.C205T:p.R69C 521 0.68 1 0.0009
ETV5 chr3 c.C287T:p.S96F 3463 0.52 0.999 NA
CSF1R a chr5 c.G1237A:p.G413S 2295 0.28 0.972 0.01
ROS1 chr6 c.C3326T:p.S1109 L 3660 0.07 0.014 0.05
NACA chr12 c.A445G:p.K149E 2927 0.38 0.999 0.07
ZNF668 chr16 c.G31A:p.D11N 3067 0.38 . NA
BRCA1 a chr17 c.A926G:p.Q309R 2105 0.06 0.999 0.03
TP53 a chr17 c.A241G:p.K81E 1475 0.11 1 NA
3
BRCA2 c.G8107A
ERCC3 chr2 c.C2111T:p.S704 L 59 0.29 0.642 0.0018
TET2 chr4 c.C86G:p.P29R 62 0.25 0.993 0.09
PALLD chr4 c.A127T:p.T43S 142 0.62 0.992 0.0005
PDGFRB chr5 c.C1223G:p.S408C 51 0.33 1 0.0005
MLLT4 chr6 c.A1264G:p.I422V 29 0.24 0.963 0.01
ROS1 chr6 c.A1611G:p.I537M 61 0.44 0.275 0.07
KIAA1549 chr7 c.G2800A:p.D934N 30 0.47 0.89 0.03
PTPRD a chr9 c.C2983T:p.R995C 44 0.44 0.321 0.05
NUP98 chr11 c.C3424G:p.Q1142E 38 0.54 0.359 0.06
TRIP11 chr14 c.G2134A:p.E712K 37 0.27 0.979 0.01
MC1R b chr16 c.G178 T:p.V60 L 34 0.32 0.988 0.05
4
BRCA1
c.G5215A
MYOC chr1 c.G227A:p.R76K 1834 0.37 0.984 0.08
ROS1 chr6 c.G500A:p.R167Q 2239 0.46 0.908 0.06
FGFR1OP a chr6 c.T760C:p.S254P 1276 0.66 0.007 0.03
FGFR1OP a chr6 c.C470T:p.T157I 2039 0.68 0.868 0.09
FGFR1OP a chr6 c.G672 T:p.K224 N 1821 0.70 0.001 0.09
KIAA1549 chr7 c.G2800A:p.D934N 1214 0.47 0.89 0.03
TRIM24 chr7 c.C2514G:p.D838E 3339 0.46 0.743 0.0027
RET b chr10 c.C1946T:p.S649 L 1054 0.44 1 0.0009
NUP98 chr11 c.C3424G:p.Q1142E 2139 0.54 0.359 0.06
HNF1A chr12 c.C293T:p.A98V 280 0.32 0.752 0.02
MC1R b chr16 c.G178 T:p.V60 L 700 0.32 0.988 0.05
5
BRCA1
c.A2841T
MUC1 chr1 c.G586A:p.G196S 2460 0.45 0.669 0.01
PAX3 b chr2 c.C941A:p.T314K 3586 0.42 0.837 0.0041
PAX8 chr2 c.T985C:p.F329 L 2362 0.47 0.924 0.01
HECW1 chr7 c.A3692G:p.N1231S 4508 0.46 0.998 0.0014
WRN chr8 c.G340A:p.V114I 3761 0.54 0.002 0.06
PTPRD a chr9 c.C2983T:p.R995C 3365 0.44 0.321 0.07
NUP98 chr11 c.C3424G:p.Q1142E 3553 0.54 0.359 0.06
CASC5 chr15 c.A4339G:p.T1447A 4457 0.40 0.336 0.05
IGF1R b chr15 c.G1532A:p.R511Q 3795 0.43 0.476 0.0009
CBFA2T3 chr16 c.G308C:p.R103P 2797 0.43 0.811 0.04
SPECC1 chr17 c.C579G:p.S193R 2353 0.60 1 0.1
SSX1 chrX c.A149G:p.Y50C 7574 0.46 0.97 0.0006
6
BRCA1
c.187delAG
FCRL4 chr1 c.C34T:p.P12S 49 0.28 0.941 0.0046
MYOC chr1 c.G227A:p.R76K 24 0.37 0.984 0.01
KIAA1549 chr7 c.G2800A:p.D934N 35 0.47 0.89 0.03
LTBP3 chr11 c.C1313T:p.A438V 24 0.25 0.997 0.05
NUP98 chr11 c.C3424G:p.Q1142E 27 0.54 0.359 0.06
BRCA2 b chr13 c.A865C:p.N289H 103 0.20 0.991 0.06
BRCA2 b chr13 c.A2971G:p.N991D 50 0.18 0 0.06
ERCC4 chr16 c.G1244A:p.R415Q 52 0.48 1 0.03
MC1R b chr16 c.G178 T:p.V60 L 17 0.32 0.988 0.05
CHD6 chr20 c.C7165T:p.R2389C 29 0.53 1 0.006
7
BRCA1
c.187delAG
PDE4DIP chr1 c.A6002G:p.E2001G 927 0.58 0.999 0.1
PPARG b chr3 c.C34G:p.P12A 923 0.46 0 0.07
ROS1 chr6 c.G500A:p.R167Q 968 0.46 0.908 0.06
ROS1 chr6 c.A1611G:p.I537M 1094 0.44 0.275 0.07
PMS2 b chr7 c.G59A:p.R20Q 877 0.45 0.924 0.07
HNF1A chr12 c.C293T:p.A98V 182 0.32 0.752 0.02
CBFA2T3 chr16 c.G308C:p.R103P 676 0.43 0.811 0.04
8
BRCA1
c.3109insAA
PDE4DIP chr1 c.A6002G:p.E2001G 42 0.58 0.999 0.1
FGFR1OP a chr6 c.C470T:p.T157I 29 0.69 0.868 0.03
FGFR1OP a chr6 c.T760C:p.S254P 22 0.66 0.007 0.03
ROS1 chr6 c.G500A:p.R167Q 29 0.46 0.908 0.06
RET b chr10 c.C1946T:p.S649 L 13 0.44 1 0.0009
NUP98 chr11 c.G4759A:p.E1587K 25 0.79 1 0.01
NUP98 chr11 c.C3424G:p.Q1142E 23 0.54 0.359 0.06
BLM chr15 c.C2603T:p.P868L 64 0.2 0.81 0.05
9
BRCA1
c.1793 delA
FANCD2 chr3 c.A1634G:p.N545S 1102 0.27 0.06 0.0046
FGFR1OP chr6 c.G688C:p.A230P 1640 0.38 0.934 0.02
ROS1 chr6 c.A1611G:p.I537M 1497 0.44 0.275 0.07
AKAP9 chr7 c.G4519C:p.D1507H 1623 0.45 0.874 0.0005
MYC chr8 c.A77G:p.N26S 838 0.56 0.977 0.02
WRN chr8 c.C3236T:p.S1079 L 1327 0.29 0.405 0.02
CARS chr11 c.G38A:p.R13H 626 0.79 1 0.0032
NUP98 chr11 c.G4759A:p.E1587K 952 0.79 1 0.01
BRCA2 b chr13 c.A865C:p.N289H 1907 0.20 0.991 0.06
BRCA2 b chr13 c.A2971G:p.N991D 1331 0.18 0 0.06
TSC2 b chr16 c.G1100A:p.R367Q 557 0.58 0.999 0.02
ASXL1 chr20 c.C3692T:p.S1231F 1399 0.55 0.03 0.02
CHD6 chr20 c.C7165T:p.R2389C 1628 0.53 1 0.01
10
BRCA2
c.6794 insA
ROS1 chr6 c.G500A:p.R167Q 22 0.46 0.908 0.06
NUP98 chr11 c.C3424G:p.Q1142E 10 0.54 0.359 0.06
OMD chr9 c.G662A:p.S221 N 41 0.46 0 0.03
ARNT chr1 c.T1506G:p.D502E 18 0.44 0.018 0.01
PAX3 chr2 c.C941A:p.T314K 14 0.42 0.837 0.02
ARHGEF12 chr11 c.A2861T:p.Y954F 68 0.33 0.01 0.05
PALB2 chr16 c.G2993A:p.G998E 71 0.27 1 0.01
EZH2 chr7 c.G436C:p.D146H 76 0.66 0.898 0.07
11
BRCA2
c.6174 del T
PAX3 b chr2 c.C941A:p.T314K 109 0.42 0.837 0.02
PPARG b chr3 c.C34G:p.P12A 49 0.46 0 0.07
PMS2 b chr7 c.G59A:p.R20Q 76 0.45 0.924 0.07
MC1R chr16 c.G178 T:p.V60 L 34 0.32 0.988 0.05
MYOC chr1 c.G227A:p.R76K 84 0.37 0.984 0.08
PTPRD a chr9 c.C2983T:p.R995C 44 0.44 0.321 0.07
SSX1 chrX c.A149G:p.Y50C 192 0.46 0.97 0.0006
MUC1 chr1 c.G586A:p.G196S 110 0.45 0.669 0.01
FANCD2 chr3 c.G521A:p.R174Q 34 0.21 0.96 0
CNTRL chr9 c.C6221A:p.A2074D 34 0.83 0.8 0.0041
PDE4DIP chr1 c.G2838A:p.M946I 25 0.59 0.028 0.09
PDE4DIP chr1 c.G4111A:p.V1371I 78 0.24 0.012 0.07
  1. aVariant annotated in the Catalogue of Somatic Mutations in Cancer (COSMIC)
  2. bVariant annotated ClinVar (NCBI Clinical Variant Database)
  3. cVariant frequencies of 0.5 ± 0.05 or 1.0 ± 0.05 may be germline
  4. dPolyphen algorithm score for predicting damaging mutations (non-Mendelian) (1 = most severe; http://genetics.bwh.harvard.edu/pph2/)
  5. eFrequency reported in the combined 1000 genomes database