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Table 2 Characterization of germline variants found among Norwegian familial CRC individuals

From: Identification of genetic variants for clinical management of familial colorectal tumors

Patient_ID

VUS (Class 3)

Benign or Likely Benign variants (Class 1 or 2)

Polymorphisms

Total variants/patient

3222

NOTCH3 NM_000435: c.5854G >A, p.V1952 M(rs115582213)b POLE NM_006231: c.3046G > A, p.V1016 M (rs147692158)

ATM NM_000051: c.5071A > C, p.S1691R (rs1800059) BRCA1 NM_007300: c.5019G > A, p.M1673I (rs1799967) PALB2 NM_024675: c.2993G > A, p.G998E (rs45551636)

PALB2 NM_024675: c.2014G > C, p.E672Q (rs45532440)

rs459552, rs659243, rs2240308, rs1799966, rs16942, rs16941, rs169547, rs4986764, rs1805107, rs506504, rs832582,

rs5868032, rs1042821, rs3219484, rs1044009, rs152451, rs2228006, rs1805321, rs4796033, rs1042522, rs861539, rs13125836

28

3308

NBN NM_002485: c.1720 T > A, p.L574I (rs142334798)POLE NM_006231:c.4523G > A, p.R1508H (rs142508245)

BARD1N M_000465: c.1075_1095del, p.L359-P365delLPECSSP (rs28997575)

rs459552, rs659243, rs11528010, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs702689, rs832582, rs5868032, rs1799977, rs1042821, rs3219484, rs1805794, rs1044009, rs2228006, rs5744934, rs5744751, rs4796033, rs1042522

24

3387

na

CDKN2AN M_000077: c.442G > A, p.A148T (rs3731249)

rs459552, rs659243, rs1801516, rs2240308

rs2070094, rs2229571, rs11528010, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs702689, rs832582, rs5868032, rs3219489, rs1044009, rs2228006, rs1805321, rs5744934, rs1042522

23

3426

na

na

rs459552, rs659243, rs1801516, rs2240308, rs2070094, rs2229571, rs1048108, rs11528010, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs702689, rs832582, rs5868032, rs1805794, rs1044009, rs2228006, rs1805321, rs1042522, rs13125836

23

4932

NOTCH3 NM_000435: c.5854G >A, p.V1952 M (rs115582213)a STK11NM_00045:c.841C > A, p.P281T (rs377208033)

na

rs459552, rs659243, rs1801516, rs2240308, rs2229571, rs11528010, rs1799966, rs16942, rs16941, rs799917, rs144848, rs169547, rs1805107, rs506504, rs12642536, rs702689, rs832582, rs5868032, rs3219489, rs1805794, rs1044009, rs2228006, rs1805321, rs861539

26

5324

na

na

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs12642536, rs832582, rs1799977, rs3219489, rs1044009, rs2228006, rs1805321, rs5744934

19

6174

na

PMS2 NM_000535: c.1454C > A, p.T485 K (rs1805323)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs1048108, rs1799966, rs16942, rs16941, rs799917, rs4986850, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs12642536, rs702689, rs832582, rs5868032, rs1799977, rs3219484, rs1805794, rs1044009, rs2228006, rs1805321, rs1042522, rs861539

29

6977

na

BARD1 NM_000465: c.1075_1095del, p.L359-P365delLPECSSP (rs28997575) BARD1NM_000465: c.1972C > T, p.R658C (rs3738888) BRCA2 NM_000059: c.9976A > T, p.K3326X (rs11571833)

rs459552, rs659243, rs1801516, rs2240308, rs1799966, rs16942, rs16941, rs799917, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs12642536, rs702689, rs832582, rs3219489, rs1044009, rs2228006, rs5744934, rs1042522, rs861539, rs28908468

27

9876

PSMC3IP NM_016556: c.136G > A, p.V46 M (rs757057684) RAD51B NM_133509: c.1063G > A, p.A355T (rs61758785)

RAD51D NM_002878: c.698A > G, p.E233G (rs28363284)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs169547, rs4986764, rs1805107, rs506504, rs702689, rs832582, rs5868032, rs1799977, rs1042821, rs1805794, rs1044009, rs2228006, rs1726801

21

9998

na

MSH6 NM_000179: c.2633 T > C, p.V878A (rs2020912)

rs459552, rs659243, rs1801516, rs2240308, rs2070094, rs2229571, rs1048108, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs12642536, rs702689, rs832582, rs5868032, rs1799977, rs1044009, rs2228006, rs1805321, rs5744751, rs1042522

24

10,675

na

PMS2 NM_000535: c.1531A > G, p.T511A (rs2228007)

rs459552, rs659243, rs1801516, rs2070094, rs2229571, rs11528010, rs1799966, rs16942, rs16941rs799917, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs702689, rs832582,rs5868032, rs1799977, rs1805794, rs1044009, rs2228006, rs10254120, rs1042522

26

12,954

MUTYH NM_012222: c.812G > A, p.R271Q (rs149866955) RAD51C NM_058216: c.790G > A, p.G264S (rs147241704)

PMS2 NM_000535: c.1789A > T, p.T597S (rs1805318)

rs459552, rs659243, rs2240308, rs2229571, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs12642536, rs702689, rs832582, rs5868032, rs1044009, rs2228006, rs1805321, rs1726801, rs4796033, rs1042522

22

13,072

BRCA1 NM_007300: c.4315C > T, p.L1439F (rs781260818)

PMS2 NM_000535: c.1531A > G, p.T511A (rs2228007)

rs459552, rs659243, rs1801516, rs2240308, rs2070094, rs2229571, rs11528010, rs1799966, rs16942, rs16941, rs799917, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs12642536, rs702689, rs832582, rs5868032, rs1799977, rs1805794, rs1044009, rs2228006, rs5744751, rs1042522

29

14,930

na

PALB2 NM_024675: c.925A > G, p.I309V (rs3809683)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs1048108, rs1799966, rs16942, rs16941, rs799917, rs4986850, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs12642536, rs702689, rs832582, rs5868032, rs1799977, rs3219489, rs1805794, rs1044009, rs152451, rs2228006, rs1805321, rs5744934, rs1042522

30

18,843

MSH6 NM_000179.2: c.2195G > A, p.R732Q (rs749746725)

BRCA1 NM_007300: c.3119G > A, p.S1040 N (rs4986852)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs11528010, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs12642536, rs832582, rs5868032, rs1799977, rs3219489, rs1044009, rs2228006, rs1805321, rs5744934, rs5744751, rs1042522, rs861539

26

19,411

na

BARD1 NM_000465: c.1972C > T, p.R658C (rs3738888) PALB2 NM_024675: c.1010 T > C, p.L337S (rs45494092)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs1799966, rs16942, rs16941, rs799917, rs4986850, rs144848, rs169547, rs1805107, rs506504, rs1126497, rs12642536, rs702689, rs832582, rs5868032, rs1805794, 1,044,009, rs2228006, rs1805321, rs5744751, rs1042522, rs861539

28

19,673

AXIN2 NM_004655: c.344A > G, p.N115S (rs370257532)

APC NM_001127510: c.7504G > A, p.G2502S (rs2229995) PMS2 NM_000535: c.1454C > A, p.T485 K (rs1805323)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs1799966, rs16942, rs16941, rs799917, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs702689, rs832582, rs5868032, rs1042821, rs1805794, rs1044009, rs2228006, rs1805321, rs4796033, rs1042522, rs861539, rs3218536

29

20,612

na

CDKN2A NM_000077: c.442G > A, p.A148T (rs3731249)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs11528010, rs1799966, rs16942, rs16941, rs799917, rs169547, rs4986764, rs1805107, rs506504, rs12642536, rs702689, rs5868032, rs1799977, rs1805794, rs1044009, rs2228006, rs1805321, rs10254120, rs5744934, rs4796033, rs1042522, rs861539

28

21,368

MAP3K1 NM_005921: c.764A > G, p.N255S (rs56069227)

ATM NM_000051: c.2572 T > C, p.F858 L (rs1800056)

rs459552, rs659243, rs2240308, rs2229571, rs11528010, rs1799950, rs169547, rs1805107, rs506504, rs1126497, rs702689, rs832582, rs5868032, rs1799977, rs1044009, rs2228006, rs1805321, rs5744934, rs4796033, rs1042522

22

22,295

na

BRCA1 NM_007300: c.5019G > A, p.M1673I (rs1799967) BRIP1 NM_032043: c.890A > G, p.K297R (rs28997570)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs1048108, rs1799966, rs16942, rs16941, rs799917, rs144848, rs169547, rs1805107, rs506504, rs12642536, rs702689, rs832582, rs5868032, rs1799977, rs1042821, rs3219489, rs1805794, rs1044009, rs2228006, rs1805321, rs5744934, rs1042522, rs861539

30

23,761

na

na

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs11528010, rs1799966, rs16942, rs16941, rs799917, rs1799950, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs702689, rs832582, rs5868032, rs1799977, rs1044009, rs2228006, rs1805321, rs1802683, rs1042522

26

23,910

na

BRCA2 NM_000059: c.6100C > T, p.R2034C (rs1799954) MSH2 NM_000251: c.965G > A, p.G322D (rs4987188) MSH6 NM_000179: c.2633 T > C, p.V878A (rs2020912) PALB2 NM_024675: c.2794G > A, p.V932 M (rs45624036) PMS2 NM_000535: c.1454C > A, p.T485 K (rs1805323) BARD1 NM_000465: c.1670G > C, p.C557S (rs28997576)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs11528010, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs702689, rs832582, rs5868032, rs1799977, rs1042821, rs1805794, rs2228006, rs10254120, rs1042522, rs13125836, rs3218536

28

24,140

na

BRCA1 NM_007300: c.5019G > A, p.M1673I (rs1799967) PMS2 NM_000535: c.1531A > G, p.T511A (rs2228007)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs1048108, rs1799966, rs16942, rs16941, rs799917, rs144848, rs169547, rs1805107, rs506504, rs1126497, rs702689, rs832582, rs5868032, rs1799977, rs1042821, rs3219489, rs1805794, rs1044009, rs2228006, rs10254120, rs5744751, rs1042522

29

24,447

CHEK2 NM_007194: c.74 T > C, p.V25A (rs587780188)

NOTCH3 NM_000435: c.3399C > A, p.H1133Q (rs112197217)

rs459552, rs659243, rs1801516, rs2240308, rs2070094, rs2229571, rs1799966, rs16942, rs16941, rs799917, rs169547, rs1805107, rs506504, rs1126497, rs702689, rs832582, rs5868032, rs1805794, rs1044009, rs2228006, rs1805321, rs1042522

24

11,705

ATM NM_000051: c.4375G > A, p.G1459R (rs145667735) MSH2 NM_000251: c.1284C > G, p.H428Q (rs776034412)

MSH2 NM_000251: c.965G > A, p.G322D (rs4987188) PMS2 NM_000535: c.1454C > A, p.T485 K (rs1805323)

rs459552, rs659243, rs1801516, rs2229571, rs11528010, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs702689, rs832582

rs5868032, rs1799977, rs3219489, rs1805794, rs1044009, rs2228006, rs1805321, rs5744751, rs1042522, rs861539, rs13125836

27

12,673

na

ATM NM_000051: c.2572 T > C, p.F858 L (rs1800056) PMS2 NM_000535: c.1454C > A, p.T485 K (rs1805323)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs1048108, rs1799950, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs12642536, rs702689, rs832582, rs5868032, rs1799977, rs1044009, rs2228006, rs1805321, rs1802683, rs4796033, rs1042522, rs861539

26

13,393

NBN NM_002485.4: c.643C > T, p.R215W (rs34767364)

BARD1 NM_000465: c.1972C > T, p.R658C (rs3738888) BRIP1 NM_032043: c.577G > A, p.V193I (rs4988346) PMS2 NM_000535: c.1531A > G, p.T511A (rs2228007) ATM NM_000051: c.4258C > T, p.L1420F (rs1800058) NOTCH3 NM_000435.2: c.3058G > C, p.A1020P (rs35769976) NOTCH3 NM_000435: c.3547G > A, p.V1183 M (rs10408676)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs1799966, rs16942, rs16941, rs799917, rs169547, rs4986764, rs1805107, rs506504, rs702689, rs832582, rs5868032, rs1805794, rs1044009, rs2228006, rs1805321, rs1042522

28

14,963

PALB2 NM_024675: c.232G > A, p.V78I (rs515726085)

PALB2 NM_024675: c.2590C > T, p.P864S (rs45568339) STK11 NM_000455: c.1062C > G, p.F354 L (rs59912467)

rs659243, rs1801516, rs2240308, rs2070094, rs2229571, rs11528010, rs1799966, rs16942, rs16941, rs799917, rs1799950, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs12642536, rs702689, rs5868032, rs1799977, rs3219489, rs1805794, rs1044009, rs2228006, rs1805321, rs5744751, rs1042522, rs861539, rs3218536

33

19,609a

na

BRCA2 NM_000059: c.4258G > T, p.D1420Y (rs28897727) POLE NM_006231: c.2083 T > A, p.F695I (rs5744799)

rs459552, rs659243, rs2240308, rs2229571, rs1799966, rs16942, rs16941, rs799917, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs702689, rs832582, rs5868032, rs1799977, rs3219484, rs1805794, rs1044009, rs2228006, rs1805321, rs5744934, rs1042522, rs13125836

28

22,953

NOTCH3 NM_000435: c.5208G > C, p.E1736D (rs200331646) MSH2 NM_000251: c.128A > G, p.Y43C (rs17217723) RAD51B NM_133510: c.515 T > G, p.L172 W (rs34094401)

BRCA2 NM_000059: c.2971A > G, p.N991D (rs1799944) CDH1 NM_004360: c.1774G > A, p.A592T (rs35187787)

rs459552, rs659243, rs2240308, rs2229571, rs11528010, rs1799966, rs16942, rs16941, rs799917, rs169547, rs4986764, rs1805107, rs506504, rs12642536, rs702689, rs832582, rs5868032, rs1042821, rs3219489, rs1805794, rs1044009, rs2228006, rs1805321, rs1726801

29

24,789

APC NM_001127510: c.4334C > T, p.T1445I (rs760686348) PALB2 NM_024675: c.1250C > A, p.S417Y (rs45510998)

BARD1 NM_000465: c.1972C > T, p.R658C (rs3738888) PALB2 NM_024675: c.2993G > A, p.G998E (rs45551636) PALB2 NM_024675: c.2014G > C, p.E672Q (rs45532440) POLE NM_006231: c.776G > A, p.R259H (rs61732929) NOTCH3 NM_000435: c.3399C > A, p.H1133Q (rs112197217)

rs459552, rs659243, rs2240308, rs2229571, rs1799966, rs16942, rs16941, rs799917, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs12642536, rs702689, rs832582, rs5868032, rs1799977, rs3219489, rs1044009, rs152451, rs2228006, rs1042522

30

25,167

NBN NM_002485.4: c.643C > T, p.R215W (rs34767364)

ATM NM_000051: c.2119 T > C, p.S707P (rs4986761)

rs459552, rs659243, rs2240308, rs2229571, rs11528010, rs169547, rs4986764, rs1805107, rs506504, rs12642536, rs702689, rs832582, rs5868032, rs1799977, rs1805794, rs2228006, rs1805321, rs1726801, rs4796033, rs1042522

22

5597

MAP3K1 NM_005921: c.2816C > G, p.S939C (rs45556841)

ATM NM_000051: c.5071A >C, p.S1691R (rs1800059)

rs459552, rs659243, rs1801516, rs2070094, rs2229571, rs11528010, rs1799966, rs16942, rs16941, rs799917, rs4986850, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs12642536, rs702689, rs832582, rs5868032, rs1042821, rs1805794, rs1044009, rs2228006, rs1805321, rs1042522

29

8913

RAD51B NM_133509: c.1063G > A, p.A355T (rs61758785) EPCAM NM_002354: c.267G > C, p.Q89H (rs146480420)

PMS2 NM_000535: c.1454C > A, p.T485 K (rs1805323)

rs459552, rs659243, rs2240308, rs2070094, rs2229571, rs1048108, rs11528010, rs1799966, rs16942, rs16941, rs799917, rs144848, rs169547, rs4986764, rs1805107, rs506504, rs1126497, rs702689, rs832582, rs5868032, rs1805794, rs1044009, rs2228006, rs5744751, rs1042522, rs861539, rs13125836

30

  1. a Recently classified as Benign by ACMG Guidelines, 2015
  2. b Patient ID carrying CHEK2 c.470 T > C, p.I157T