Table 7 Pathogenic or likely pathogenic CNVs found in the cohort

#6

VSD,

–

Facial dysmorphisms

del

arr[hg19] 3q29(194,654,896–197,363,564) × 1

P

TFRC

Chromosome 3q29 microdeletion syndrome

#20

TOF

–

Respiratory system

del

arr[hg19] 22q11.1q11.21(17,900,000–20,600,000) × 1

P

ATP6V1E1, PEX26,TUBA8

22q11 deletion syndrome

#23

PVS

–

–

del

arr[hg19] 2p25.3(50–450,000) × 1

P

–

–

#24

Complex CHD

–

–

dup

arr[hg19] 15q24.3q25.2(78,250,000–85,000,000) × 1

P

ARNT2, RPS17,AP3B2

Chromosome 15q25 deletion syndrome

#35

Complex CHD

–

–

del

arr[hg19] 5p15.33p14.2(20,000–23,980,000) × 3

P

SDHA, NDUFS6

Mitochondrial complex II deficiency, Leigh syndrome(LS)

#35

Complex CHD

–

–

dup

arr[hg19] 21(q22.12-q22.3)(37,780,000–48,100,000) × 3

P

–

Down syndome

#39

PAA

–

–

del

arr[hg19] 7q11.23(72,260,000–76,000,000) × 3

P

POR

7q11.23 duplication syndrome,

WILLIAMS-BEUREN region duplication syndrome

#41

d-TGA

–

–

dup

arr[hg19] 1p36.33p36.32(820,000–3,320,000) × 3

LP

AGRN,B3GALT6, TMEM240

congenital myasthenic syndrome-8 (CMS8), Ehlers-Danlos syndrome progeroid type 2

#56

DORV, PAA

–

–

del

arr[hg19] 5p15.33p15.1(20,000–16,500,000) × 1

P

SDHA

5p15 terminal (Cri du chat syndrome) region duplication,mitochondrial complex II deficiency[OMIM:252011]

#56

DORV,PAA

–

–

dup

arr[hg19] 17q24.2q25.3(65,320,000–81,160,000)) × 3

P

PSMD12

46 XX sex reversal 2,

STANKIEWICZ-ISIDOR syndrome(STISS)

#59

AVSD

–

–

del

arr[hg19] 20p12.3(6,300,001–8,580,000) × 3

LP

BMP2

BRACHYDACTYLY, TYPE A2(BDA2),

Early infantile epileptic encephalopathy-12 (EIEE12)

#78

VSD + ASD

Single umbilical artery

Facial Dysmorphisms

del

arr[hg19] 7p22.3p22.1(40,000–6,740,000) × 1

LP

BRAT1

lethal neonatal rigidity and multifocal seizure syndrome

#78

VSD + ASD

Single umbilical artery

Facial dysmorphisms

dup

arr[hg19] 12p13.33p13.31(160,000–8,320,000) × 3

LP

CACNA1C, CCND2, CHD4

Timothy syndrome(TS),

SIFRIM-HITZ-WEISS syndrome (SIHIWES)

#82

TOF

–

–

dup

arr[hg19] 8p23.1(6,920,000–12,580,000) × 3

P

–

8p23.1 duplication syndrome

#84

TOF

–

–

del

arr[hg19] 22q11.21(18,880,000–21,440,000) × 1

P

PRODH

DIGEORGE syndrome; DGS (proximal, A-B)syndrome1,

#85

VSD, IAA

–

–

del

arr[hg19] 22q11.21q11.23(18,564,800–24,300,000) × 1

P

PEX26, TUBA8,PRODH

22q11 deletion syndrome

#100

TOF

–

–

del

arr[hg19] 22q11.21(18,970,561–21,800,471) × 1

P

CLTCL1, HIRA,TBX1

DiGeorgesyndrome(DGS), velocardio facial syndrome(VCFS)

#110

Other CHD

–

Central nervous

del

arr[hg19] 7q33q36.3(137,754,586–159,119,707) × 1

P

BRAF, CNTNAP2, DPP6

Cardiofaciocutaneous syndrome-1, Noonan syndrome 7,

#110

Other CHD

–

Central nervous

dup

arr[hg19] 20q13.2q13.33(51,222,942–62,913,645) × 3

P

CYP24A1, PCK1,OSBPL2, RTEL1

HYPERCALCEMIA INFANTILE-1(HCINF1),

phosphoenolpyruvate carboxykinase deficiency

#111

VSD

–

–

del

arr[hg19] 16p11.2(29,428,531–30,190,029) × 1

LP

PRRT2, KCTD13, TBX6, MAPK3

16p11.2deletion syndrome

#114

AS

–

Skeletal system

del

arr[hg19] 22q11.21(18,631,364–21,800,471) × 1

P

CLTCL1,HIRA,TBX1

DiGeorgesyndrome(DGS),

velo- cardio- facial syndrome(VCFS)

#116

CA, VSD, PLSVC

–

Cystic hygroma, Skeletal system

del

arr[hg19] 4p16.3p15.31(68,345–18,451,423) × 1

P

LONP1, NFIX, SMARCA4

BWS/SRS (Beckwith–Wiedemann syndrome/Silver-Russell syndrome;CODAS syndrome

#116

CA, VSD, PLSVC

–

Cystic hygroma, Skeletal system

dup

arr[hg19] 11p15.5p15.1(230,680–20,167,667) × 3

P

APC2,TICAM1, LONP1

Pigmented nodular adrenocortical diseaseprimarysyndrome;

CODAS syndrome

#117

Other CHD

Echogenic bowel

Skeletal system

del

arr[hg19] 15q11.2(22,770,421–23,277,436) × 1

LP

TUBGCP5, CYFIP1, NIPA2, NIPA1

15q11.2 recurrent region (BP1-BP2) (includes NIPA1) deletionsyndrome1

#120

Other CHD

Choroid plexus cysts

Facial dysmorphisms

dup

arr[hg19] Xp22.31(6,455,151–8,135,568) × 3

P

PUDP, STS, VCX, PNPLA4

Steroid sulphatase deficiency (STS)

#121

PAA,ASD

–

Urinary tract system, facial dysmorphisms

del

arr[hg19] 4q31.3(151,335,416–151,834,016) × 1

LP

LRBA, MAB21L2

–

#135

CA

–

–

del

arr[hg19] 21q22.2q22.3(39,985,071–48,093,361) × 1

P

KPTN

Autosomal recessive mental retardation-41 (MRT41)

#136

VSD

–

–

dup

arr[hg19] 9q34.11q34.3(133,343,703–141,018,648) × 3

P

–

–

#138

AVSD

–

–

del

arr[hg19] 16q24.1q24.2(85,520,919–87,149,214) × 1

P

FOXF1, FOXC2, FOXL1

–

#157

VSD, IAA

–

–

del

arr[hg19] 22q11.21(18,636,749–21,800,471) × 1

P

CLTCL1, HIRA,TBX1

DiGeorgesyndrome(DGS), velo- cardio- facial syndrome(VCFS)

#179

VSD

–

–

del

arr[hg19] 15q11.2(22,770,421–23,625,785) × 1

LP

TUBGCP5, CYFIP1, NIPA2, NIPA1

15q11.2 recurrent region (BP1-BP2)deletionsyndrome

#179

VSD

–

–

del

arr[hg19] 16p13.11(14,910,158–16,520,463) × 1

P

NOMO1, NPIPA1, PDXDC1, NTAN1), RRN3, KIAA0430, NDE1, MYH11, ABCC1, ABCC6, NOMO3

16p13.11 recurrent microdeletion syndrome