Table 3. Putative deleterious rare CNVs in this cohort.

Sample	Cytoband	CNV	Inheritance	Authors' classification	Phenotype
DE61OSOUKBD100197	2q13	hg19 chr2:g.(111186302_111667198)_(113094793_113273657)dup	U	Uncertain – likely pathogenic	OA/TOF, sister as unilateral renal agenesis, both patient and sister are otherwise healthy
SKZ_1248	4q35.2	hg19 chr4:g.(187540292_187318091)_(187318091_187849681)dup	M	Uncertain – likely pathogenic	OA/TOF, pyloric stenosis; dysmorphisms, hearing loss
SKZ_1856	6p22.3	hg19 chr6:g.(20884837_20901311)_(20901267_21082258)del	NP	Uncertain – likely pathogenic	OA/TOF, septal defect, club foot
SKZ_1855	11p15.4	hg19 chr11:g.(4371631_4391231)_(5132119_5253127)dup	NP	Uncertain – likely pathogenic	OA/TOF
SKZ_0856	15q13.3	hg19 chr15:g.(32457092_32457092)_(32514341_32771537)del	P	Uncertain – likely pathogenic	OA/TOF, anal atresia, bifid/fused ribs, coarctation, abnormal arterial supply right lung, abnormal sacrum
SKZ_1150	16p13.11	hg19 chr16:g.(15539023_15545022)_(16282307_16291541)dup	P	Uncertain – likely pathogenic	OA/TOF+ atrioventricular septal defect
SKZ_1988	16p13.11	hg19 chr16:g.(15034035_15092778)_(15998820_16106095)dup	P	Uncertain – likely pathogenic	OA/TOF, anal anomalies
SKZ_1780	22q11.21	hg19 chr22:g.(18637139_18640300)_(20286099_20289862)dup	M	Uncertain – likely pathogenic	OA/TOF, anal atresia, ventricular septal defect
SKZ_0680	Xp22.2	hg19 chrX:g.(10299643_10302384)_(10637327_10638042)del	M	Pathogenic	Laryngo-tracheo-oesophageal-cleft, hypospadias, dysmorphims, hypotonia, pyloric stenosis; opitz syndrome

Abbreviations: M, inheritance – maternal; NP, no parental DNA available; NZ, nullizygous; P, inheritance – paternal; U, inheritance – undetermined.

Total number of putative deleterious CNVs in the Erasmus MC – Sophia, Baylor College of Medicine and University of Bonn OA/TOF cohort (=375). Chromosome region according to build hg19. All CNVs were absent from our in-house control cohort.