Table 2 Pathogenic variants of BRCA2 and their frequencies in the general Japanese population (ToMMo:54KJPN)

c.632-1G>A

Splice site

8

Splicing

rs81002820

1/108558

9.212 ×10⁻⁶

Pathogenic

c.657_658del

c.658_659del

p.V220Ifs*4

8

Frameshift

rs80359604

1/108568

9.211 ×10⁻⁶

2.352 ×10⁻⁵

4.601 ×10⁻⁵

Pathogenic

c.1023_1027del

p.C341*

10

Nonsense

1/108586

9.209 ×10⁻⁶

Pathogenic (E)

c.1274del

c.1278del

p.D427Tfs*3

10

Frameshift

rs80359274

2/108574

1.842 ×10⁻⁵

Pathogenic

c.1389_1390del

p.V464Gfs*3

10

Frameshift

rs80359283

1/108584

9.209 ×10⁻⁶

2.741 ×10⁻⁶

Pathogenic

c.1399del

c.1400del

p.K467Rfs*18

10

Frameshift

1/108582

9.210 ×10⁻⁶

Pathogenic (E)

c.1776T>G

p.Y592*

10

Nonsense

1/108602

9.208 ×10⁻⁶

Pathogenic (E)

c.1794_1798del

c.1796_1800del

p.S599*

10

Nonsense

rs276174813

1/108604

9.208 ×10⁻⁶

2.750 ×10⁻⁶

Pathogenic

c.1806del

c.1813del

p.I605Yfs*9

10

Frameshift

rs80359306

6/108604

5.525 ×10⁻⁵

9.657 ×10⁻⁶

2.524 ×10⁻⁵

6.597 ×10⁻⁶

1.932 ×10⁻⁴

Pathogenic

c.1806_1807del

c.1812_1813del

p.K604Nfs*11

10

Frameshift

1/108604

9.208 ×10⁻⁶

Pathogenic (E)

c.1888dup

p.T630Nfs*6

10

Frameshift

rs80359314

1/108604

9.208 ×10⁻⁶

6.860 ×10⁻⁷

Pathogenic

c.2073del

c.2076del

p.K692Nfs*38

11

Frameshift

1/108604

9.208 ×10⁻⁶

Pathogenic (E)

c.2582dup

c.2588dup

p.N863Kfs*18

11

Frameshift

rs80359335

1/108572

9.210 ×10⁻⁶

4.865 ×10⁻⁶

2.528 ×10⁻⁵

6.579 ×10⁻⁶

Pathogenic

c.2622dup

p.V875Cfs*6

11

Frameshift

rs886038076

1/108578

9.210 ×10⁻⁶

Pathogenic

c.2806_2809del

c.2808_2811del

p.A938Pfs*21

11

Frameshift

rs80359351

4/108574

3.684 ×10⁻⁵

2.121 ×10⁻⁵

2.523 ×10⁻⁵

1.314 ×10⁻⁵

Pathogenic

c.2830A>T

p.K944*

11

Nonsense

rs80358533

1/108568

9.211 ×10⁻⁶

3.421 ×10⁻⁶

6.569 ×10⁻⁶

Pathogenic

c.3086dup

p.M1029Ifs*7

11

Frameshift

rs2072472083

1/108568

9.211 ×10⁻⁶

Pathogenic/Likely pathogenic

c.3846_3847del

c.3847_3848del

p.V1283Kfs*2

11

Frameshift

rs80359405

1/108470

9.219 ×10⁻⁶

3.722 ×10⁻⁵

7.239 ×10⁻⁵

1.925 ×10⁻⁴

Pathogenic

c.3854_3855del

c.3859_3860del

p.N1287*

11

Nonsense

rs80359406

1/108470

9.219 ×10⁻⁶

Pathogenic

c.4020del

c.4021del

p.S1341Qfs*33

11

Frameshift

rs397507702

1/108440

9.222 ×10⁻⁶

Pathogenic

c.4339del

p.V1447*

11

Nonsense

rs80359443

6/108442

5.533 ×10⁻⁵

Pathogenic

c.4461_4462del

c.4464_4465del

p.H1488Qfs*25

11

Frameshift

rs397507720

4/108402

3.690 ×10⁻⁵

Pathogenic

c.4588dup

c.4593dup

p.V1532Sfs*2

11

Frameshift

rs397507731

3/108420

2.767 ×10⁻⁵

3.182 ×10⁻⁶

Pathogenic

c.4770_4771del

c.4772_4773del

p.C1591*

11

Nonsense

rs2072512484

2/108396

1.845 ×10⁻⁵

Pathogenic

c.4822G>T

p.E1608*

11

Nonsense

rs1566231194

1/108414

9.224 ×10⁻⁶

1.591 ×10⁻⁶

2.773 ×10⁻⁵

Likely pathogenic

c.5000C>G

p.S1667*

11

Nonsense

rs397507346

1/108418

9.224 ×10⁻⁶

Pathogenic

c.5066del

p.A1689Efs*17

11

Frameshift

1/108404

9.225 ×10⁻⁶

Pathogenic

c.5067dup

c.5073dup

p.W1692Mfs*3

11

Frameshift

rs80359479

2/108400

1.845 ×10⁻⁵

3.895 ×10⁻⁵

2.537 ×10⁻⁵

1.979 ×10⁻⁵

Pathogenic

c.5211_5214del

c.5213_5216del

p.T1738Ifs*2

11

Frameshift

rs80359493

1/108462

9.220 ×10⁻⁶

6.867 ×10⁻⁶

Pathogenic

c.5241_5242insAGCT

c.5243_5246dup

p.Y1749*

11

Nonsense

1/108440

9.222 ×10⁻⁶

Pathogenic (E)

c.5308_5309insCTGGTATTGAG

c.5310_5320dup

p.P1774Lfs*7

11

Frameshift

1/108444

9.221 ×10⁻⁶

Pathogenic (E)

c.5327T>A

p.L1776*

11

Nonsense

1/108430

9.223 ×10⁻⁶

Pathogenic (E)

c.5479_5483del

c.5482_5486del

p.K1828Vfs*4

11

Frameshift

rs80359516

1/108442

9.222 ×10⁻⁶

Pathogenic

c.5574_5577del

c.5576_5579del

p.I1859Kfs*3

11

Frameshift

rs80359520

23/108464

2.121 ×10⁻⁴

1.927 ×10⁻⁵

1.515 ×10⁻⁴

1.316 ×10⁻⁵

1.924 ×10⁻⁴

Pathogenic

c.5635G>T

p.E1879*

11

Nonsense

rs55996097

2/108466

1.844 ×10⁻⁵

Pathogenic

c.5674del

c.5675del

p.G1892Vfs*17

11

Frameshift

rs1593906164

4/108480

3.687 ×10⁻⁵

Pathogenic

c.5681dup

p.Y1894*

11

Nonsense

rs80359527

1/108478

9.218 ×10⁻⁶

2.053 ×10⁻⁶

2.521 ×10⁻⁵

Pathogenic

c.5718_5719del

c.5722_5723del

p.L1908Rfs*2

11

Frameshift

rs80359530

1/108508

9.216 ×10⁻⁶

1.505 ×10⁻⁵

5.042 ×10⁻⁵

Pathogenic

c.5728dup

c.5729dup

p.N1910Kfs*2

11

Frameshift

1/108502

9.216 ×10⁻⁶

Pathogenic (E)

c.6085G>T

p.E2029*

11

Nonsense

rs397507828

1/108546

9.213 ×10⁻⁶

Pathogenic

c.6140dup

p.Y2047*

11

Nonsense

1/108548

9.213 ×10⁻⁶

Pathogenic

c.6402_6406del

c.6405_6409del

p.N2135Kfs*3

11

Frameshift

rs80359584

3/108558

2.763 ×10⁻⁵

2.065 ×10⁻⁵

7.577 ×10⁻⁵

1.314 ×10⁻⁵

Pathogenic

c.6438_6441del

c.6440_6443del

p.H2147Lfs*20

11

Frameshift

rs1566234607

5/108562

4.606 ×10⁻⁵

Pathogenic (E)

c.6482_6485del

c.6486_6489del

p.K2162Nfs*5

11

Frameshift

rs80359598

1/108576

9.210 ×10⁻⁶

9.720 ×10⁻⁶

1.972 ×10⁻⁵

Pathogenic

c.6516del

p.V2174Lfs*17

11

Frameshift

rs2072558268

4/108576

3.684 ×10⁻⁵

Pathogenic/Likely pathogenic

c.6552del

c.6553del

p.A2185Lfs*6

11

Frameshift

rs80359603

1/108578

9.210 ×10⁻⁶

1.373 ×10⁻⁶

2.524 ×10⁻⁵

Pathogenic

c.6656C>A

p.S2219*

11

Nonsense

1/108588

9.209 ×10⁻⁶

Pathogenic

c.6666C>G

p.Y2222*

11

Nonsense

1/108690

9.209 ×10⁻⁶

Pathogenic (E)

c.6715G>T

p.E2239*

11

Nonsense

rs276174876

1/108600

9.208 ×10⁻⁶

Pathogenic

c.6893dup

c.6896dup

p.N2299Kfs*41

12

Frameshift

rs886040933

1/108514

9.215 ×10⁻⁶

Conflicting

c.6922A>T

p.K2308*

12

Nonsense

3/108520

2.764 ×10⁻⁵

Conflicting

c.6952C>T

p.R2318*

13

Nonsense

rs80358920

37/108476

3.411 ×10⁻⁴

1.031 ×10⁻⁵

3.548 ×10⁻⁴

Pathogenic

c.7585del

c.7586del

p.G2529Afs*22

15

Frameshift

rs2072699136

1/108604

9.208 ×10⁻⁶

Pathogenic

c.7601_7602ins^a

p.S2536_I3418delinsY

15

Deletion

1/108604

9.208 ×10⁻⁶

Pathogenic (E)

c.7605_7606insGGAGC

p.S2536Gfs*17

15

Frameshift

1/108604

9.208 ×10⁻⁶

Pathogenic (E)

c.7606_7607ins^b

p.S2536_I3418delinsYPSSSP

15

Deletion

1/108604

9.208 ×10⁻⁶

Pathogenic (E)

c.7615C>T

p.Q2539*

15

Nonsense

rs886040720

3/108604

2.762 ×10⁻⁵

3.181 ×10⁻⁶

2.773 ×10⁻⁵

Pathogenic

c.7671_7672del

c.7673_7674del

p.E2558Vfs*7

16

Frameshift

rs80359672

1/108604

9.208 ×10⁻⁶

1.591 ×10⁻⁶

Pathogenic

c.7806-2A>T

Splice site

17

Splicing

rs81002836

1/108604

9.208 ×10⁻⁶

Pathogenic/Likely pathogenic

c.7806-2A>G

Splice site

17

Splicing

rs81002836

1/108604

9.208 ×10⁻⁶

Pathogenic

c.8023A>G

p.I2675V

18

Missense

rs397507954

5/108596

4.604 ×10⁻⁵

1.591 ×10⁻⁶

2.773 ×10⁻⁵

Pathogenic

c.8167G>C

p.D2723H

18

Missense

rs41293511

1/108590

9.209 ×10⁻⁶

1.368 ×10⁻⁵

6.571 ×10⁻⁶

Pathogenic

c.8243G>A

p.G2748D

18

Missense

rs80359071

3/108594

2.763 ×10⁻⁵

3.420 ×10⁻⁶

Pathogenic

c.8504C>A

p.S2835*

20

Nonsense

rs80359102

2/108604

1.842 ×10⁻⁵

Pathogenic

c.8629G>T

p.E2877*

20

Nonsense

rs80359121

2/108604

1.842 ×10⁻⁵

Pathogenic

c.8713_8716del

p.Y2905Kfs*3

21

Frameshift

rs80359726

1/108604

9.208 ×10⁻⁶

Pathogenic

c.9076C>T

p.Q3026*

23

Nonsense

rs80359159

1/108582

9.210 ×10⁻⁶

2.053 ×10⁻⁶

5.044 ×10⁻⁵

Pathogenic

c.9090del

c.9097del

p.T3033Lfs*29

23

Frameshift

rs397507419

2/108586

1.842 ×10⁻⁵

Pathogenic

c.9117G>A

p.P3039=

23

Splicing

rs28897756

3/108590

2.763 ×10⁻⁵

3.422 ×10⁻⁶

6.574 ×10⁻⁶

Pathogenic

c.9154C>T

p.R3052W

24

Missense

rs45580035

1/108600

9.208 ×10⁻⁶

5.473 ×10⁻⁶

Pathogenic

c.9501+1G>T

Splice site

25

Splicing

rs397508058

1/108570

9.211 ×10⁻⁶

Pathogenic/Likely pathogenic