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["Supplementary Table 15. Small CNVs from DSD Cohort versus Small CNVs from DGV and ClinGen Databases"]
["Genea","Exons, Intronsb","ID #","Size (kbp)","Marker Count","Type","CN State","DGVc ","ClinGend"]
["AHRR","exon 5","D12",14.484,18,"Loss",1,"2/2 African (605 bp)","benign"]
["AHRR","exons 5-6 ","D17",19.77,19,"Loss",1,"2/2 African (605 bp)","benign"]
["AHRR","intron 4","D16",8.766,14,"Loss",1,"none ","benign"]
["AHRR","intron 4","D21",8.766,14,"Loss",1,"none ","benign"]
["ANOS1","intron 2","D40",7,18,"Gain",2,"none ","LB (107, 287 Kb)"]
["ANOS1","entire gene ","D3","entire gene","entire gene","Loss",1,"none ","NA"]
["AR","intron 1 ","D31",8.381,16,"Gain",2,"none ","none"]
["AR","exons 2-8 (intron 1)","D3",190.517,86,"Loss",1,"none ","none"]
["ARX","entire gene ","D44",23,5,"Gain",4,"none ","none "]
["ATRX","entire gene ","D10 ","entire gene","entire gene","Gain",2,"none ","none"]
["ATRX","intron 23 ","D30",5.187,12,"Gain",3,"none ","none"]
["ATRX","intron 23 ","D37",2.206,10,"Gain",2,"none ","none"]
["AXIN1","exon 5","D34",6.579,16,"Loss",1,"none ","none "]
["AXIN1","exon 5","D44",6.579,16,"Loss",1,"none ","none "]
["AXIN1","exon 5","D52",6.579,16,"Loss",1,"none ","none "]
["AXIN1","exons 4-5","D42",12.735,44,"Loss",1,"none ","none "]
["AXIN1","intron 4","D51",2.087,8,"Loss",1,"none ","none "]
["BBS9","exon 1  (RP9)","D21",30,12,"Gain",3,"1748/875 (2.5 Mb)","VOUS 16.9 Kb exon 1 (benign 20 Kb upstream)"]
["BNC2","intron 1","D36",1.93,5,"Gain",4,"none ","LB"]
["BNC2","intron 1","D12",3.702,12,"Loss",1,"none ","none "]
["BNC2","intron 1","D15",3.702,12,"Loss",1,"none ","none "]
["BNC2","intron 2","D52",2.069,8,"Loss",1,"none ","none "]
["CAMK1D","intron 1","D20",6,8,"Loss",1,"none ","none "]
["CHD7","intron 1","D9",2,3,"Gain",4,"none ","pathogenic (189 Kb)"]
["CHD7","exons 35-38","D1",11.4,9,"Loss",1,"2/2 (1.1 Kb)","pathogenic (189 Kb)"]
["CNTNAP3","entire gene ","D18","entire gene","entire gene","Gain",3,"653/492 (2 Mb)","LB (140 Kb)"]
["CNTNAP3","exons 1-2","D15",95.708,17,"Gain",3,"653/492 (2 Mb)","LB (140 Kb)"]
["CNTNAP3","exons 19-24","D14",374.048,66,"Gain",3,"653/492 (2 Mb)","LB (75 Kb)"]
["CREBBP","intron 2","D4",5,7,"Loss",1,"516/439 (444 Kb)","pathogenic (155 Kb)"]
["CTNNA3","intron 5","D37",6.612,5,"Gain",4,"none ","none "]
["CTNNA3","intron 7","D21",15.582,18,"Gain",3,"none ","none "]
["CTNNA3","intron 7","D14",14.283,15,"Gain",4,"none ","none "]
["CTNNA3","intron 13","D27",7.416,8,"Loss",1,"none ","benign (109 Kb)"]
["CTNNA3","intron 9","D46",22.158,12,"Loss",1,"none ","benign (73, 120 Kb)"]
["CTNNA3","intron 12 ","D10",31.747,33,"Loss",1,"none ","benign (82, 179 Kb)"]
["CTNNA3","exon 10 near 5'","D43",92.181,104,"Loss",1,"2/2 (38 Kb)","benign(37, 176, 205 Kb)"]
["CTNNB1","exons 8-17","D18",19.067,43,"Gain",3,"none ","none "]
["CTNNB1","exons 9-14","D21",9.628,13,"Gain",4,"none ","none "]
["CTNNB1","exons 9-15","D16",10.332,27,"Gain",3,"none ","none "]
["CTNNB1","exons 9-15","D17",10.332,27,"Gain",3,"none ","none "]
["CTNNB1","intron 1 ","D14",12.571,59,"Gain",3,"none ","none "]
["CXCL12","disrupted exon 4 (3')","D17",6.895,10,"Gain",4,"none ","none"]
["CXCL12","exon 4","D21",8.082,12,"Gain",3,"none ","none"]
["DHRSX","intron 3","D25",1.174,28,"Gain",3,"none ","benign (551 Kb)"]
["DHRSX","intron 3","D31",1.118,27,"Gain",4,"none ","LB (551 Kb)"]
["DHRSX","intron 1 ","D36",9.178,48,"Gain",3,"none ","none"]
["DHRSX","intron 1 ","D45",16.755,95,"Gain",3,"none ","none"]
["DHRSX","intron 3","D46",24.485,52,"Loss",1,"254/248 (2.8 Kb)","benign (171 Kb)"]
["DHRSX","intron 1 ","D25",5.369,37,"Loss",1,"common 33.6 Kb 235/205 ","none "]
["DHRSX","intron 1 ","D25",3.006,35,"Loss",1,"common 33.6 Kb 235/205 ","none "]
["DHRSX","intron 1 ","D26",14.427,84,"Loss",1,"common 33.6 Kb 235/205 ","none "]
["DHRSX","intron 1 ","D32",1.195,15,"Loss",1,"common 33.6 Kb 235/205 ","none "]
["DHRSX","intron 1 ","D41",2.047,28,"Loss",1,"common 33.6 Kb 235/205 ","none "]
["DHRSX","intron 1 ","D48",14.715,83,"Loss",1,"common 33.6 Kb 235/205 ","none "]
["DHRSX","intron 1 ","D51",1.858,12,"Loss",1,"common 33.6 Kb 235/205 ","none "]
["DHRSX","exon 3","D26",1.343,8,"Loss",1,"none ","none "]
["DHRSX","exons 2-3","D46",48.838,106,"Loss",1,"none ","none "]
["DHRSX","intron 3","D40",1.831,12,"Loss",1,"none ","none "]
["DMD","intron 1","D34",5.571,21,"Gain",3,"none ","LB (851 kb)"]
["DMD","intron 1 ","D36",3.874,13,"Gain",2,"none ","LB (851 kb)"]
["DMD","intron 1 ","D30",5.569,20,"Gain",2,"none ","LB (851 kb)"]
["DMD","intron 2 ","D28",9.609,18,"Gain",2,"31/30 (1.9 Kb)","none"]
["DMD","exons 75-76","D30",5.031,14,"Gain",2,"none ","none"]
["DMD","intron 2 ","D23",2.449,16,"Gain",2,"none ","none"]
["DMD","intron 2 ","D37",2.449,16,"Gain",2,"none ","none"]
["DMD","intron 2 ","D30",9.618,22,"Gain",2,"none ","none"]
["DMD","intron 44","D30",17.369,48,"Gain",2,"none ","none"]
["DMD","intron 44","D29",3.509,11,"Gain",4,"none ","none"]
["DMD","intron 44","D34",3.728,12,"Gain",4,"none ","none"]
["DMD","intron 44","D44",3.731,15,"Gain",4,"none ","none"]
["DMD","intron 59","D34",1.395,10,"Gain",4,"none ","none"]
["DMD","intron 59","D42",1.395,10,"Gain",2,"none ","none"]
["DMD","intron 59","D44",1.395,10,"Gain",4,"none ","none"]
["DMD","intron 59","D52",1.395,10,"Gain",4,"none ","none"]
["DMD","intron 60 ","D34",2.239,18,"Gain",4,"none ","none"]
["DMD","intron 60 ","D30",2.371,20,"Gain",4,"none ","none"]
["DMD","intron 62","D31",6.423,20,"Gain",2,"none ","none"]
["DMD","intron 7","D31",1.623,12,"Gain",2,"none ","none"]
["DMD","intron 74","D29",1.973,11,"Gain",4,"none ","none"]
["DMD","intron 74","D44",2.695,12,"Gain",4,"none ","none"]
["DMD","exon 48","D41",5.741,12,"Loss",0,"none ","LB (28 Kb)"]
["DMD","exon 48","D23",5.023,7,"Loss",0,"none ","LB (28 Kb)"]
["DMD","exon 48","D50",5.159,11,"Loss",0,"none ","LB (28 Kb)"]
["DMD","intron 17","D48",6.299,40,"Loss",0,"2/2 (3.5 Kb)","none"]
["DMD","intron 17","D52",6.299,40,"Loss",1,"2/2 (3.5 Kb)","none"]
["DMD","intron 2 ","D38",4.432,9,"Loss",0,"31/30 (1.9 Kb)","none"]
["DMD","intron 2 ","D32",2.617,12,"Loss",0,"432/426 (3.1 Kb)","none"]
["DMD","exon 18","D40",1.686,6,"Loss",0,"none ","none"]
["DMD","exons 40-41","D41",3.89,15,"Loss",0,"none ","none"]
["DMD","exons 8-9","D52",3.564,8,"Loss",1,"none ","none"]
["DMD","exons 8-9","D29",3.633,12,"Loss",1,"none ","none"]
["DMD","intron 1 ","D29",4.061,12,"Loss",1,"none ","none"]
["DMD","intron 2 ","D29",9.823,20,"Loss",1,"none ","none"]
["DMD","intron 55","D42",2.816,16,"Loss",0,"none ","none"]
["DMD","intron 55","D52",2.816,16,"Loss",0,"none ","none"]
["DMD","intron 55","D48",9.647,36,"Loss",0,"none ","none"]
["DMD","intron 55","D52",1.303,20,"Loss",1,"none ","none"]
["DMD","intron 55","D44",9.846,52,"Loss",1,"none ","none"]
["DMD","intron 59","D48",2.172,6,"Loss",0,"none ","none"]
["DMD","intron 59 ","D20",1.177,5,"Loss",0,"none ","none"]
["DMD","intron 60 ","D52",1.519,24,"Loss",1,"none ","none"]
["DMD","intron 60 ","D29",3.142,26,"Loss",1,"none ","none"]
["DMD","intron 60 ","D51",4.72,22,"Loss",1,"none ","none"]
["DMD","intron 60 ","D44",5.495,24,"Loss",1,"none ","none"]
["DMD","intron 62","D38",2.775,8,"Loss",0,"none ","none"]
["DMD","intron 7","D40",1.085,28,"Loss",0,"none ","none"]
["DMD","intron 7","D29",1.111,24,"Loss",1,"none ","none"]
["DMD","intron 7","D52",1.88,39,"Loss",1,"none ","none"]
["DMD","intron 9 ","D52",2.014,10,"Loss",1,"none ","none"]
["DMD","intron 9 ","D29",7.032,25,"Loss",1,"none ","none"]
["DMD","intron 9 ","D48",5.091,16,"Loss",0,"none ","none"]
["DMD","intron 9 ","D42",5.099,18,"Loss",0,"none ","none"]
["EP300","exons 7-8","D29",3.107,16,"Gain",4,"none ","none "]
["EP300","exons 7-8","D48",3.107,16,"Gain",4,"none ","none "]
["EP300","exons 8-10","D13",3.581,14,"Loss",1,"none ","pathogenic (87 Kb)"]
["ESR1","intron 7","D30",25,8,"Gain",3,"none ","none "]
["ESR1","intron 7","D27",28,28,"Loss",1,"none ","none "]
["ESR2","disrupted exon 13 ","D15",1.805,26,"Gain",3,"none ","none "]
["ESR2","disrupted exon 13 ","D16",1.805,26,"Gain",3,"none ","none "]
["ESR2","exon 13","D21",7.276,38,"Gain",3,"none ","none "]
["ESR2","exon 9","D42",4.786,8,"Gain",4,"none ","none "]
["ESR2","exon 9","D44",4.786,8,"Gain",4,"none ","none "]
["ESR2","exon 9","D34",10.456,12,"Gain",4,"none ","none "]
["ESR2","exons 7-8","D13",8.583,21,"Gain",3,"none ","none "]
["ESR2","exon 9","D13",12.839,19,"Loss",1,"none ","none "]
["ESR2","intron 12","D1",2.983,12,"Loss",1,"none ","none "]
["ESR2","intron 12","D9",3.243,18,"Loss",1,"none ","none "]
["ESR2","intron 12","D10",3.383,17,"Loss",1,"none ","none "]
["ESR2","intron 12","D13",3.607,21,"Loss",1,"none ","none "]
["ESR2","intron 9 ","D42",1.469,12,"Loss",1,"none ","none "]
["FAM167A-AS1 (C8orf12)","intron 1","D13",15.888,18,"Loss",1,"14/14 (914 bp)","none"]
["FAM167A-AS1 (C8orf12)","intron 1","D14",19.164,20,"Loss",1,"14/14 (914 bp)","none"]
["FGD1","exons 13-18  (WNK3, PHF8, FAM120C)","D3",507,184,"Loss",1,"773/404 (2.8 Mb)","none "]
["FGF7 ","exons 3-4 (FAM227B)","D51",139,112,"Loss",1,"none ","none "]
["FGFR2","intron 5","D38",6,6,"Gain",4,"none ","none "]
["FGFR2","exons 14-15","D4",6,9,"Loss",1,"none ","none "]
["FLNA","exons 6-48","D1",22.858,40,"Gain",3,"none ","LB (42 Kb)"]
["FLNA","disrupted exon 22; exons 22-48","D21",16.012,37,"Gain",2,"none ","none"]
["FLNA","disrupted exon 48","D9",10.732,23,"Gain",2,"none ","none"]
["FLT1","exon 24","D4",2.417,8,"Loss",1,"none ","none "]
["FLT1","intron 3","D4",11.378,5,"Loss",1,"none ","none "]
["FRAS1 ","exon 30","D22",11.475,8,"Loss",1,"none ","none "]
["FRAS1 ","exon 30","D24",11.475,8,"Loss",1,"none ","none "]
["FRAS1 ","exon 30","D26",11.475,8,"Loss",1,"none ","none "]
["FRAS1 ","exon 30","D42",11.475,8,"Loss",1,"none ","none "]
["FRG1BP","entire gene ","D15",121.375,25,"Gain",3,"212/208 gain loss (234 Kb)","none "]
["FRG1BP","entire gene ","D18",345.158,45,"Gain",3,"212/208 gain loss (234 Kb)","none "]
["GATA4","intron 2","D12",7,14,"Loss",1,"28/28 (338 bp)","none "]
["GFRA1","exon 5","D14",18.277,19,"Gain",3,"none ","none "]
["GFRA1","exon 5","D19",21.989,21,"Gain",3,"none ","none "]
["GNRH1","entire gene  (DOCK5, KCTD9, CDCA2)","D13",64,52,"Gain",3,"none ","none "]
["GRIP1 ","intron 5","D5",8.432,11,"Gain",4,"none ","none "]
["GRIP1 ","exon 14","D1",15.333,12,"Loss",1,"none ","none "]
["GRIP1 ","intron 1","D15",23.926,15,"Loss",1,"none ","none "]
["HHAT","intron 7","D31",3,8,"Loss",1,"none ","none "]
["HSD17B3","intron 2 ","D18",7,4,"Gain",4,"none ","none "]
["INSR","disrupted exon 22 (with ZNF557)","D14",29.054,23,"Loss",1,"none ","benign (187, 233 Kb)"]
["INSR","intron 2 ","D24",13.98,16,"Loss",1,"none ","none "]
["KANK1 ","exon 6","D18",32.062,41,"Gain",3,"none ","benign (173, 404 Kb)"]
["KANK1 ","intron 6","D17",15.615,15,"Gain",3,"none ","benign (173, 404 Kb)"]
["KANK1 ","intron 6","D20",5.594,12,"Gain",3,"none ","benign (173, 404 Kb)"]
["KANK1 ","intron 6","D16",5.354,7,"Gain",4,"none ","benign (173, 404 Kb)"]
["KANK1 ","intron 5","D43",4.123,8,"Loss",1,"77/39 (18 Kb)","none "]
["KRAS","disrupted exon 4","D2",4.197,20,"Gain",3,"none ","none "]
["KRAS","disrupted exon 4; exons 4-5","D7",12.167,35,"Gain",3,"none ","none "]
["KRAS","disrupted exon 4","D6",8.5,29,"Gain",3,"none ","none "]
["KRAS","disrupted exon 4","D19",8.5,29,"Gain",3,"none ","none "]
["MOV10L1","exons 16-19","D33",9.97,8,"Loss",1,"none ","none "]
["MOV10L1","exons 16-19","D35",9.97,8,"Loss",1,"none ","none "]
["MOV10L1","exons 16-19","D37",9.97,8,"Loss",1,"none ","none "]
["MOV10L1","exons 16-19","D46",9.97,8,"Loss",1,"none ","none "]
["MOV10L1","intron 2 ","D13",6.774,7,"Loss",1,"none ","none "]
["MOV10L1","intron 2 ","D14",4.586,5,"Loss",1,"none ","none "]
["MTHFR ","entire gene (CLCN6)","D15",31,14,"Loss",1,"none ","none "]
["NLGN4X","intron 2 ","D25",2.038,12,"Gain",2,"none ","none"]
["NLGN4X","intron 2 ","D31",1.526,12,"Gain",2,"none ","none"]
["NLGN4X","intron 2 ","D29",1.53,16,"Gain",4,"none ","none"]
["NLGN4X","intron 2 ","D34",1.53,16,"Gain",4,"none ","none"]
["NLGN4X","entire gene ","D10","entire gene","entire gene","Gain ",2,"NA","NA"]
["NLGN4X","intron 2 ","D44",1.53,16,"Loss",1,"none ","none"]
["NLGN4X","intron 3","D40",3.23,12,"Loss",0,"none ","none "]
["NLGN4X","intron 3","D48",3.109,7,"Loss",0,"none ","none "]
["NLGN4X","intron 3","D29",4.77,23,"Loss",1,"none ","none "]
["NOTCH1","intron 2","D29",4.371,8,"Loss",0,"common 16/15 (1.2 Kb); common 6/6 (760 bp)","none "]
["NOTCH1","intron 2","D32",4.371,8,"Loss",0,"common 16/15 (1.2 Kb); common 6/6 (760 bp)","none "]
["NOTCH1","intron 2","D52",4.371,8,"Loss",0,"common 16/15 (1.2 Kb); common 6/6 (760 bp)","none "]
["NOTCH2","intron 1","D41",29,38,"Loss",1,"610/558 (170 Kb)","benign (78 Kb)"]
["NOTCH3","exons 13-33","D6",27.041,38,"Gain",3,"common 2/2 (143 bp)","none "]
["NOTCH3","exon 1","D16",2.786,9,"Gain",4,"none ","none "]
["NOTCH3","exon 1","D17",2.786,9,"Gain",4,"none ","none "]
["NOTCH3","exon 1","D18",2.786,9,"Gain",4,"none ","none "]
["NOTCH3","exon 1","D19",2.495,6,"Gain",4,"none ","none "]
["NOTCH3","exons 1-20","D21",22.15,47,"Gain",3,"none ","none "]
["NOTCH3","exons 2-20","D12",19.822,46,"Gain",3,"none ","none "]
["NOTCH3","exons 2-20","D15",19.822,46,"Gain",3,"none ","none "]
["NR0B1","disrupted exon 1 ; exons 1-2","D30",4.932,32,"Gain",2,"none ","pathogenic 5 Kb loss"]
["NR0B1","entire gene ","D28",5.64,39,"Gain",2,"none ","pathogenic 5 Kb loss"]
["NR0B1","entire gene ","D10","entire gene","entire gene","Gain ",2,"none ","pathogenic 5 Kb loss"]
["NR5A1","exons 1-4 (NR6A1)","D9",18,5,"Loss",1,"none ","26 Kb (pathogenic)"]
["NR5A2","intron 5","D25",1.112,6,"Loss",1,"none ","none "]
["NR5A2","intron 7","D25",4.529,14,"Loss",1,"none ","none "]
["NR5A2","intron 7","D28",2.896,10,"Loss",1,"none ","none "]
["OCA2","intron 19","D16",11.157,11,"Gain",4,"none ","LB (531 Kb)"]
["OCA2","intron 19","D18",11.157,11,"Gain",4,"none ","LB (531 Kb)"]
["OCA2","intron 19","D21",11.157,11,"Gain",4,"none ","LB (531 Kb)"]
["OCA2","intron 2 ","D42",2.422,8,"Gain",4,"none ","LB (531 Kb)"]
["OCA2","intron 23 ","D21",29.279,24,"Gain",3,"none ","LB (531 Kb)"]
["PBX1","intron 2 ","D38",7.081,5,"Gain",4,"none ","none "]
["PBX1","intron 2 ","D34",1.253,8,"Gain",4,"none ","none "]
["PBX1","intron 2 ","D42",1.253,8,"Gain",4,"none ","none "]
["PBX1","intron 2 ","D44",1.253,8,"Gain",4,"none ","none "]
["PBX1","intron 2 ","D48",1.253,8,"Gain",4,"none ","none "]
["PCDH17","intron 3","D5",6.653,7,"Loss",1,"none ","none "]
["PCDH17","intron 3","D9",6.653,7,"Loss",1,"none ","none "]
["PCSK1","entire gene ","D9","entire gene","entire gene","Loss",1,"none ","benign (79 Kb)"]
["PCSK1","exons 1-3","D10",24.849,18,"Loss",1,"none ","none "]
["PDGFRA","disrupted exon 23 ","D6",2.859,22,"Gain",3,"none ","none "]
["PDGFRA","exons 13-23","D18",18.881,66,"Gain",3,"none ","none "]
["PDGFRA","exons 13-23","D21",18.881,66,"Gain",3,"none ","none "]
["PDGFRA","exons 13-23","D17",18.745,61,"Gain",3,"none ","none "]
["PIP5K1B","intron 7","D15",1.665,3,"Gain",4,"none ","none"]
["PIP5K1B","intron 7","D18",1.665,3,"Gain",4,"none ","none"]
["PIP5K1B","intron 9","D27",3.522,8,"Gain",4,"none ","none"]
["PIP5K1B","exon 13","D46",4.136,5,"Loss",1,"none ","none"]
["POR","intron 1","D23",15,9,"Loss",1,"none ","none "]
["PTCH1","exons 1-2","D42",4.356,20,"Gain",4,"163/162 gain loss (87 Kb)","none"]
["PTCH1","intron 2 ","D4",14.621,34,"Gain",3,"163/162 gain loss (87 Kb)","none"]
["PTCH1","intron 2 ","D7",16.368,40,"Gain",3,"163/162 gain loss (87 Kb)","none"]
["PTCH1","intron 2 ","D12",3.713,31,"Gain",3,"163/162 gain loss (87 Kb)","none"]
["PTCH1","exons 11-12","D21",4.117,13,"Gain",4,"none ","none"]
["PTCH1","exons 14-15","D21",4.047,19,"Gain",4,"none ","none"]
["PTPN11","exons 11-16","D14",37.014,38,"Gain",3,"none ","none "]
["PTPN11","exons 11-16","D15",37.014,38,"Gain",3,"none ","none "]
["PTPN11","exons 11-16","D16",37.014,38,"Gain",3,"none ","none "]
["PTPN11","exons 11-16","D18",37.014,38,"Gain",3,"none ","none "]
["PTPN11","exons 11-16","D21 ",37.014,38,"Gain",3,"none ","none "]
["PTPN11","exon 1 (RPL6)","D24",16.373,8,"Loss",1,"2/2 (1.4 Kb)","none "]
["RAF1","intron 1 ","D7",3.837,11,"Gain",4,"none ","benign (92 Kb)"]
["RAF1","exons 3-6","D18",13.598,32,"Gain",3,"none ","LB (147, 161 Kb)"]
["RAF1","intron 1 ","D7",8.433,11,"Loss",1,"86/68 (966 Kb)","none "]
["ROCK2","exons 31-33 (PQLC3)","D15",42.161,19,"Loss",1,"none ","none "]
["ROCK2","intron 1","D1",28.091,15,"Loss",1,"none ","none "]
["SHOX","exons 4-6","D12",41.547,10,"Gain",4,"none ","benign (521 Kb)"]
["SHOX","entire gene ","D10","entire gene","entire gene","Gain",3,"NA","NA"]
["SHOX","exon 6","D46",41.663,81,"Loss",1,"5/5 (566 bp)","none "]
["SNRPN","exon 3 (introns 2, 3)","D12",36.457,34,"Gain",3,"none ","benign (15 Kb)"]
["SNRPN","intron 2","D21",14.752,17,"Gain",3,"none ","benign (15 Kb)"]
["SOS1","intron 1","D16",18,8,"Loss",1,"none ","VOUS (343 Kb); benign loss (4.5 Kb) "]
["SOX9","PE","D25",6,8,"Loss",1,"none ","none"]
["SOX9","PE","D46",6,8,"Loss",1,"none ","none"]
["SOX9","PE","D52",6,8,"Loss",1,"none ","none"]
["SOX9 ","PE (LINC00459)","D38",1.6,17,"Loss",1,"66/53 (2.9 Kb loss)","none "]
["SRD5A2","disrupted exon 6; exons 4-6","D30",6.909,8,"Loss",1,"none ","none "]
["SRD5A2","disrupted exon 6; exons 4-6","D39",6.909,8,"Loss",1,"none ","none "]
["SUPT3H","intron 2  (RUNX2)","D38",9.773,8,"Loss",0,"none ","none (pathogenic 223 Kb)"]
["SUPT3H (RUNX2)","intron 2  (RUNX2)","D48",9.989,16,"Loss",1,"none ","none (pathogenic 223 Kb)"]
["TGFB1","exons 6-7","D18",4.015,2,"Gain",4,"none ","none "]
["TGFB1","exons 6-7","D21",4.015,2,"Gain",4,"none ","none "]
["TP63","exon 7","D42",1.352,8,"Gain",4,"none ","none"]
["TP63","exons 5-7","D27",4.56,12,"Gain",4,"none ","none"]
["TP63","exons 5-7","D34",4.56,12,"Gain",4,"none ","none"]
["TP63","exons 5-7","D43",4.56,12,"Gain",4,"none ","none"]
["TP63","exons 5-7","D48 ",4.56,12,"Gain",4,"none ","none"]
["TP63","exons 5-7","D41",11.795,28,"Gain",3,"none ","none"]
["TP63","intron 1 ","D16",4.149,8,"Loss",1,"1000/567 (176 Kb)","none"]
["TP63","intron 1 ","D22",11.13,34,"Loss",1,"742/561 (9.2 Kb)","none"]
["TP63","intron 1 ","D42",3.886,34,"Loss",1,"742/561 (9.2 Kb)","none"]
["TP63","intron 1 ","D45",11.223,36,"Loss",1,"742/561 (9.2 Kb)","none"]
["TP63","intron 1 ","D38",8.299,32,"Loss",1,"742/561 (9.2 Kb)","none"]
["TP63","intron 1 ","D52",8.299,32,"Loss",1,"742/561 (9.2 Kb)","none"]
["TP63","exons 8-10","D2",10.208,12,"Loss",1,"none ","none"]
["VAMP7","exons 6-8 (3')","D46",94.31,153,"Loss",1,"562/735 gain loss (342 Kb)","benign (251 Kb)"]
["VAMP7","intron 6","D36",1.493,5,"Loss",1,"735/562 gain loss (342 Kb)","benign (251 Kb)"]
["WNT2","intron 3","D34",6,8,"Loss",1,"none ","none "]
["WWOX","intron 5","D17",52.788,56,"Gain",3,"835/603 (gain loss 16 Kb)","LB (606 Kb)"]
["WWOX","intron 5","D21",36.886,35,"Gain",3,"835/603 (gain loss 16 Kb)","LB (606 Kb)"]
["WWOX","intron 5","D33",12.391,22,"Gain",3,"835/603 (gain loss 16 Kb)","LB (606 Kb)"]
["WWOX","intron 5","D45",12.128,21,"Gain",3,"835/603 (gain loss 16 Kb)","LB (606 Kb)"]
["WWOX","intron 8","D18",14.11,20,"Gain",3,"none ","none "]
["WWOX","intron 8","D2",4.643,7,"Gain",4,"none ","none "]
["WWOX","exon 9","D45",148.179,208,"Loss",1,"none ","LB (539 Kb)"]
["WWOX","intron 4","D22",8.076,23,"Loss",1,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D29",8.165,24,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D38",8.165,24,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D39",8.165,24,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D41",8.165,24,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D43",8.165,24,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D2",8.836,12,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D8",8.836,12,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D9",8.836,12,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5"," D10",8.836,12,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D16",8.836,12,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D20",8.836,12,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D21",8.836,12,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D12",4.495,7,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D12",3.748,3,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D18",4.899,8,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D26",7.236,22,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D32",7.236,22,"Loss",0,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 5","D42",6.976,19,"Loss",1,"835/603 (gain loss 16 Kb)","none "]
["WWOX","intron 8","D14",1.795,14,"Loss",1,"98/45 (3.6 Kb)","none "]
["agene name in parenthesis - old name"]
["bentry in parenthesis - other gene included in the CNV or location of CNV"]
["cDGV small CNV inclusive and stringent data obtained by Zarrei et al (2015); includes number of variants/number of samples"]
["dLB - likely benign; VOUS - variant of uncertain significance"]