Table 3. List of rare CNVs identified in neurodevelopmental disorders.
| Chr | Start | End | Size | Chr. Band | CNV | Sample | Cohort | Type | Gene count | Inheritance | Control count | DECIPHER count | DGV count |
| chr14 | 21533898 | 22239332 | 705434 | 14q11.2 | deletion | Si238 | Autism_ID | non HS | 12 | maternal | 0 | 2 | 6 |
| chr12 | 15036168 | 29977743 | 14941575 | 12p12.3p11.2 | deletion | Si159 | Autism_ID | non HS | 3 | de novo | 0 | 0 | 0 |
| chr15 | 66881730 | 71972563 | 5090833 | 15q23q24.1 | deletion | Si169 | Autism_ID | HS assoc | 2 | de novo | 0 | 0 | 0 |
| chr3 | 59681529 | 79199503 | 19517974 | 3p14.2p12.3 | deletion | Si163 | Autism_ID | non HS | 3 | de novo | 0 | 0 | 0 |
| chr5 | 175479593 | 175584441 | 104848 | 5q35.2 | deletion | Si118 | Autism_ID | HS | 1 | paternal | 0 | 0 | 4 |
| chr7 | 31583983 | 31702682 | 118699 | 7p15.3 | duplication | Si309 | Autism_ID | HS | 2 | maternal | 0 | 0 | 2 |
| chr16 | 21645311 | 22520339 | 875028 | 16p12.1 | duplication | Si247 | Autism_No ID | HS | 3 | NA | 0 | 2 | 0 |
| chr22 | 38790464 | 39138992 | 348528 | 22q13.1 | deletion | Si126 | Autism_No ID | non HS | 4 | de novo | 0 | 1 | 0 |
| chr3 | 67276200 | 72402720 | 5126520 | 3p14.1p13 | deletion | Si140 | Autism_No ID | non HS | 2 | de novo | 0 | 1 | 1 |
| chr1 | 145303997 | 145357746 | 53749 | 1q21.1 | homozyg deletion | Si192 | Autism_No ID | HS | 0 | both | 0 | 0 | 0 |
| chr1 | 145303997 | 145357746 | 53749 | 1q21.1 | deletion | Si85 | Autism_No ID | HS | 6 | paternal | 0 | 0 | 0 |
| chr11 | 21703096 | 26791696 | 5088600 | 11p14.5 | duplication | Si45 | Autism_No ID | non HS | 0 | maternal | 0 | 0 | 0 |
| chr16 | 72859686 | 72917454 | 57768 | 16p22.3 | deletion | Si99 | Autism_No ID | HS | 5 | maternal | 0 | 0 | 0 |
| chr17 | 15301836 | 16542913 | 1241077 | 17p11.2 | duplication | Si153 | Autism_No ID | HS | 147 | paternal | 0 | 0 | 0 |
| chr17 | 32250000 | 32400000 | 150000 | 17q12 | duplication | Si114 | Autism_No ID | HS | 1 | paternal | 0 | 0 | 0 |
| chr17 | 42115600 | 42437714 | 322114 | 17q21.32 | duplication | Si186 | Autism_No ID | HS | 53 | de novo | 0 | 0 | 0 |
| chr17 | 58889277 | 59561178 | 671901 | 17q23.3 | duplication | Si87 | Autism_No ID | non HS | 1 | maternal | 0 | 0 | 0 |
| chr18 | 69039514 | 69822140 | 782626 | 18q22.3 | deletion | Si173 | Autism_No ID | non HS | 2 | maternal | 0 | 0 | 0 |
| chr19 | 14760644 | 15064029 | 303385 | 19p13.12 | deletion | Si125 | Autism_No ID | non HS | 5 | maternal | 0 | 0 | 0 |
| chr2 | 95159338 | 95228560 | 69222 | 2q11.1 | duplication | Si226 | Autism_No ID | HS | 1 | de novo | 0 | 0 | 0 |
| chr20 | 12657983 | 13311383 | 653400 | 20p12.1 | deletion | Si20 | Autism_No ID | non HS | 17 | paternal | 0 | 0 | 0 |
| chr22 | 18562002 | 18748556 | 186554 | 22q11.21 | duplication | Si207 | Autism_No ID | HS | 5 | de novo | 0 | 0 | 0 |
| chr3 | 84868129 | 85439477 | 571348 | 3p12.1 | duplication | Si128 | Autism_No ID | non HS | 73 | paternal | 0 | 0 | 0 |
| chr5 | 370492 | 1003781 | 633289 | 5p15.33 | duplication | Si82 | Autism_No ID | HS | 17 | paternal | 0 | 0 | 0 |
| chr5 | 175504664 | 175584441 | 79777 | 5q35.2 | deletion | Si191 | Autism_No ID | HS | 3 | maternal | 0 | 0 | 4 |
| chr6 | 51096930 | 51899775 | 802845 | 6p12.2 | duplication | Si142 | Autism_No ID | non HS | 4 | paternal | 0 | 0 | 0 |
| chr7 | 152102637 | 153356944 | 1254307 | 7q36.2 | duplication | Si119 | Autism_No ID | HS | 123 | paternal | 0 | 0 | 0 |
| chr7 | 153451569 | 154285634 | 834065 | 7q36.2 | deletion | Si132 | Autism_No ID | non HS | 0 | maternal | 0 | 0 | 0 |
| chr1 | 144106777 | 144451305 | 344528 | 1q21.1 | deletion | 2602 | Dyslexia | HS | 1 | NA | 2 | 3 | 0 |
| chr3 | 139732796 | 140171095 | 438299 | 3q22.3 | duplication | 1806 | Dyslexia | non HS | 142 | NA | 1 | 1 | 0 |
| chr6 | 65179840 | 66364033 | 1184193 | 6q12 | deletion | 2803 | Dyslexia | non HS | 1 | paternal | 1 | 1 | 0 |
| chr4 | 123017758 | 123458923 | 441165 | 4q27 | duplication | 2286 | Dyslexia | non HS | 0 | maternal | 0 | 0 | 0 |
| chr7 | 40606348 | 40819984 | 213636 | 7p14.1 | deletion | 2244 | Dyslexia | non HS | 1 | maternal | 0 | 0 | 0 |
| chr7 | 68820751 | 68904999 | 84248 | 7q11.22 | deletion | 2867 | Dyslexia | HS | 2 | paternal | 0 | 0 | 0 |
| chr7 | 69876932 | 70546042 | 669110 | 7q11.22 | duplication | 1102 | Dyslexia | HS | 1 | paternal | 0 | 0 | 0 |
| chr7 | 110381300 | 110851860 | 470560 | 7q31.1 | deletion | 3437 | Dyslexia | non HS | 102 | paternal | 2 | 0 | 0 |
| chr8 | 11373083 | 11434911 | 61828 | 8p23.1 | deletion | 1012 | Dyslexia | HS | 16 | maternal | 0 | 0 | 0 |
| chr9 | 6348644 | 6740836 | 392192 | 9p24.1 | deletion | 1004 | Dyslexia | non HS | 11 | paternal | 0 | 0 | 0 |
| chr9 | 1 | 9098781 | 9098780 | 9p24 | deletion | 3381 | ID | non HS | 3 | de novo | 0 | 15 | 0 |
| chr11 | 121813520 | 134447248 | 12633728 | 11q24.1-q25 | deletion | 2597 | ID | non HS | 33 | de novo | 0 | 15 | 0 |
| chr18 | 1 | 15313807 | 15313806 | 18p11.21 | duplication | 2492 | ID | non HS | 1 | de novo | 0 | 4 | 0 |
| chr9 | 73827781 | 79830447 | 6002666 | 9q21.13 | deletion | 3413 | ID | non HS | 1 | de novo | 0 | 4 | 0 |
| chr3 | 196825112 | 197208742 | 383630 | 3q29 | deletion | 3331 | ID | HS | 0 | NA | 0 | 2 | 1 |
| chr6 | 161747330 | 162612669 | 865339 | 6q26 | deletion | 2562 | ID | non HS | 0 | maternal | 0 | 2 | 0 |
| chr6 | 162129914 | 162555946 | 426032 | 6q26 | deletion | 2548 | ID | non HS | 48 | paternal | 0 | 2 | 0 |
| chr9 | 218822 | 3742630 | 3523808 | 9p24 | deletion | 2615 | ID | non HS | 1 | de novo | 0 | 2 | 0 |
| chr3 | 71242809 | 77832202 | 6589393 | 3p13 | deletion | 2509 | ID | non HS | 0 | de novo | 0 | 1 | 0 |
| chr3 | 127000260 | 131353408 | 4353148 | 3q21.3 | duplication | 2237 | ID | non HS | 1 | NA | 0 | 1 | 0 |
| chr6 | 107959196 | 111971187 | 4011991 | 6q21 | deletion | 2644 | ID | non HS | 0 | de novo | 0 | 1 | 0 |
| chrX | 146437800 | 147110597 | 672797 | Xq27 | duplication | 2643 | ID | non HS | 6 | NA | 0 | 1 | 0 |
| chrY | 6895278 | 7233586 | 338308 | Yp11.2 | duplication | 2580 | ID | non HS | 2 | NA | 0 | 1 | 0 |
| chr1 | 76466419 | 77200494 | 734075 | 1p31.1 | duplication | 3399 | ID | non HS | 0 | maternal | 0 | 0 | 0 |
| chr1 | 90483825 | 90786224 | 302399 | 1p22.2 | duplication | 1799 | ID | non HS | 48 | NA | 0 | 0 | 0 |
| chr1 | 235537560 | 237086860 | 1549300 | 1q43 | deletion | 2518 | ID | non HS | 2 | NA | 0 | 0 | 0 |
| chr10 | 128662416 | 129042087 | 379671 | 10q26.2 | deletion | 1402 | ID | non HS | 23 | maternal | 0 | 0 | 0 |
| chr11 | 22232079 | 25091772 | 2859693 | 11p14.3 | deletion | 1613 | ID | non HS | 2 | de novo | 0 | 0 | 0 |
| chr13 | 95576502 | 96051348 | 474846 | 13q31.3q32.2 | deletion | 2175 | ID | non HS | 3 | NA | 0 | 0 | 0 |
| chr14 | 40428504 | 40755943 | 327439 | 14q21.1 | duplication | 3322 | ID | non HS | 89 | NA | 0 | 0 | 1 |
| chr15 | 80767738 | 100147041 | 19379303 | 15q25 | duplication | 2522 | ID | non HS | 36 | paternal or de novo | 0 | 0 | 0 |
| chr17 | 34089604 | 34566438 | 476834 | 17q12 | duplication | 72 | ID | HS | 4 | NA | 0 | 0 | 0 |
| chr18 | 50965716 | 52820402 | 1854686 | 18q21 | duplication | 1164 | ID | non HS | 37 | de novo | 0 | 0 | 0 |
| chr19 | 60032498 | 61147051 | 1114553 | 19q13.42 | deletion | 3262 | ID | non HS | 24 | de novo | 0 | 0 | 0 |
| chr2 | 153753287 | 183588035 | 29834748 | 2q24.3q32.1 | duplication | 2559 | ID | non HS | 5 | de novo | 0 | 0 | 0 |
| chr2 | 188179827 | 188853079 | 673252 | 2q32.1 | duplication | 2522 | ID | non HS | 1 | paternal or de novo | 0 | 0 | 0 |
| chr3 | 50846910 | 58424157 | 7577247 | 3p21.31p14.3 | duplication | 3448 | ID | non HS | 54 | de novo | 0 | 0 | 0 |
| chr3 | 62489781 | 63320060 | 832020 | 3p14.2 | duplication | 3445 | ID | non HS | 413 | paternal | 0 | 0 | 0 |
| chr3 | 137464270 | 137768886 | 304616 | 3q22.3 | deletion | 3349 | ID | non HS | 25 | NA | 0 | 0 | 0 |
| chr4 | 7148184 | 7818626 | 670442 | 4p16.1 | duplication | 2488 | ID | non HS | 2 | NA | 0 | 0 | 0 |
| chr4 | 43534966 | 45590689 | 2055723 | 4p13 | deletion | 1318 | ID | non HS | 0 | paternal | 0 | 0 | 0 |
| chr4 | 57346833 | 86106712 | 28759879 | 4q12q21.33 | duplication | 2154 | ID | non HS | 2 | de novo | 0 | 0 | 0 |
| chr4 | 152300259 | 152723977 | 423718 | 4q31.3 | deletion | 699 | ID | non HS | 9 | de novo | 0 | 0 | 0 |
| chr5 | 28427525 | 28630668 | 203143 | 5p14.1 | deletion | 2569 | ID | non HS | 4 | NA | 0 | 0 | 0 |
| chr5 | 98793016 | 98851760 | 58744 | 5q21.1 | deletion | 1519 | ID | HS | 1 | NA | 0 | 0 | 0 |
| chr5 | 156526018 | 164133824 | 7607806 | 5q33.3q34 | duplication | 3448 | ID | non HS | 1 | de novo | 0 | 0 | 0 |
| chr6 | 92767349 | 92988105 | 220756 | 6q16.1 | deletion | 3316 | ID | non HS | 15 | NA | 0 | 0 | 0 |
| chr7 | 45180992 | 45274014 | 93022 | 7p13 | deletion | 3296 | ID | HS | 1 | paternal or de novo | 0 | 0 | 1 |
| chr7 | 51216627 | 51313401 | 96774 | 7p12.1 | deletion | 2571 | ID | non HS | 24 | NA | 0 | 0 | 0 |
| chr7 | 68713709 | 69068502 | 354793 | 7q11.22 | deletion | 2433 | ID | HS | 66 | NA | 0 | 0 | 0 |
| chr7 | 72300576 | 72486542 | 185966 | 7q11.23 | duplication | 2424 | ID | HS | 47 | maternal | 0 | 0 | 0 |
| chr7 | 89028789 | 89548951 | 520162 | 7q21.13 | duplication | 3352 | ID | non HS | 42 | NA | 0 | 0 | 0 |
| chr8 | 123404368 | 123637074 | 232706 | 8q24.13 | deletion | 3247 | ID | non HS | 0 | de novo | 0 | 0 | 0 |
| chr9 | 21080948 | 21484861 | 403913 | 9p21.3 | deletion | 2462 | ID | non HS | 5 | NA | 0 | 0 | 0 |
| chr9 | 38634661 | 38791196 | 156535 | 9p13.1 | deletion | 3236 | ID | HS | 0 | paternal | 0 | 0 | 0 |
| chrX | 28400903 | 28659988 | 259085 | Xp21.3 | duplication | 3321 | ID | non HS | 0 | NA | 0 | 0 | 0 |
| chrX | 65611216 | 65934000 | 322784 | Xq12 | deletion | 2597 | ID | non HS | 2 | NA | 0 | 0 | 2 |
| chrX | 88508702 | 91291323 | 2782621 | Xq21.31q31.32 | deletion | 2511 | ID | non HS | 4 | NA | 0 | 0 | 0 |
| chrY | 3072083 | 6154525 | 3082442 | Yp11.2 | duplication | 699 | ID | HS | 2 | de novo | 0 | 0 | 0 |
| chr22 | 40103633 | 41458051 | 1354418 | 22q13.2 | deletion | GB43 | ID/MCA | non HS | 2 | NA | 0 | 2 | 0 |
| chr4 | 110560125 | 113895249 | 3335124 | 4q25 | deletion | GB6 | ID/MCA | non HS | 15 | de novo | 0 | 1 | 0 |
| chr1 | 174979260 | 238257861 | 63278601 | 1q24qter | duplication | GB88 | ID/MCA | non HS | 2 | 46,XX,t(1;5)(q23;p15) balanced | 0 | 0 | 0 |
| chr13 | 83679489 | 84385310 | 705821 | 13q31.1 dup | duplication | GB71 | ID/MCA | non HS | 9 | maternal | 0 | 0 | 0 |
| chr3 | 164241146 | 168622524 | 4381378 | 3q26.1 | deletion | GB42 | ID/MCA | non HS | 11 | maternal | 0 | 0 | 0 |
| chr5 | 90252 | 1630763 | 1540511 | 5p15.33 | deletion | GB88 | ID/MCA | HS | 0 | 46,XX,t(1;5)(q23;p15) balanced | 0 | 0 | 0 |
| chr7 | 27294680 | 28799546 | 1504866 | 7p15.3 | duplication | GB65 | ID/MCA | non HS | 23 | de novo | 0 | 0 | 0 |
| chr9 | 201336 | 16672312 | 16470976 | part trisomy 9 | duplication | GB71 | ID/MCA | HS assoc | 1 | 46,XX rcp (8;10)(q2.2;q21.2)+t (9;12)(p2.2;p1.3) | 0 | 0 | 0 |
This list does not contain known genomic disorders. Please refer to Table S9 for known genomic disorders identified in this study. CNV: Copy Number Variant; ID: Intellectual Disability; HS: Hotspot; MCA: Multiple Congenital Anomalies.