Table 1.

Frequencies and penetrance for the SCZ-associated CNVs only. The full list of CNVs is presented in Supplementary Material, Table S4.

locus	Selection coefficient	Frequency %				Penetrance % (95%CI)
		controls	SCZ	DD/ASD/CM	general population	SCZ	DD/CM/ASD	Total
1q21.1 del	0.26	0.021	0.17	0.29	0.033	5.2 (2.5–11)	35 (18–67)	40 (20–78)
1q21.1 dup	0.23	0.038	0.13	0.2	0.045	2.9 (1.3–6.3)	18 (10–33)	21 (11–39)
NRXN1 del	0.23	0.02	0.18	0.18	0.028	6.4 (2.5–8.3)	26 (16–80)	33 (18–88)
3q29 del	0.83	0.0014	0.082	0.061	0.0046	18 (4.7–67)	53 (15–100)	71 (20–100)
WBS dup	0.61	0.0058	0.066	0.12	0.011	6.0 (1.4–20)	44 (13–100)	50 (14–100)
15q11.2 del	0.09	0.28	0.59	0.81	0.3	2.0 (1.4–2.7)	11 (8.2–14)	13 (9.6–17)
Prader-Willi/Angelman dup	0.5	0.0083	0.079	0.25	0.019	4.2 (1.4–12)	54 (25–100)	58 (26–100)
15q13.3 del	0.31	0.019	0.14	0.26	0.03	4.7 (2.2–9.9)	35 (19–62)	40 (21–72)
16p13.11 dup	0.13	0.13	0.31	0.3	0.14	2.2 (1.3–3.7)	8.4 (5.7–13)	10.6 (7–17)
16p11.2 distal del	0.29	0.018	0.063	0.14	0.024	2.6 (0.8–9.2)	23 (8.4–63)	26 (9.2–72)
16p11.2 dup	0.33	0.03	0.35	0.28	0.043	8.0 (4.3–14)	26 (18–43)	34 (22–57)
17q12 del	0.68	0.0054	0.036	0.087	0.009	4.0 (0.8–18)	39 (13–100)	43 (14–100)
DiGeorge/VCFS del	0.8	0	0.29	0.54	0.024	12 (6.5–18)	88 (53–100)	100 (60–100)