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Table 3 Variant details and respective classification scores for 16p11.2del CNV and CHD8 test cases

From: Functional DNA methylation signatures for autism spectrum disorder genomic risk loci: 16p11.2 deletions and CHD8 variants

Sample ID Sex Age (years) 16p11.2del coordinates (size in kb) Diagnostic classification for 16p11.2 typical deletion (pathogenic, benign, variant of unknown significance [VUS]) Inheritance ASD status 16p11.2del score
348 M 0.25 29,590,493–30,190,593 (600) Pathogenic Unknown Unknown 0.11505
228 M 0.4 29,590,493–30,190,593 (600) Pathogenic Unknown Unknown 0.12668
875 F 4 29,656,657–30,190,593 (534) Pathogenic Unknown Unknown 0.03073
172 F 6 29,590,493–30,190,593 (600) Pathogenic Unknown Unknown 0.04668
292 M 0.25 29,500,252–30,098,094 (598) Pathogenic Unknown Unknown 0.13978
2-0088-003 F 12 29,652,799–30,199,507 (547) Pathogenic (MOSAIC) De novo ASD -0.00441
3-0406-000 M 1.2 29,581,764–30,199,579 (618) Pathogenic Unknown ASD 0.07735
6-0196-03 M Unknown 29,500,084–30,098,210 (598) Pathogenic Unknown ASD 0.04815
1-0616-003 M 7.5 28,751,255–28,952,351 (201) Not determined* Maternal ASD − 0.11936
Sample ID Sex Age (years) CHD8 variant nucleotide change; amino acid change (Exon #) Diagnostic classification (pathogenic, benign, variant of unknown significance [VUS]) Inheritance ASD status CHD8+/− score
14406.p1 M 13 c.7493_7495del; p.His2498del (37) VUS De novo ASD − 0.03482
1-0494-003 M 4.75 c.2219A>G; p.Asn740Ser (9) Benign Paternal ASD − 0.04451
2-1228-003 F 4.5 c.6841C>G; p.Pro2281Ala (34) Benign Paternal ASD − 0.04178
1-0277-003 M Unknown c.6565G>A; p.Gly2189Arg (33) Benign Maternal ASD − 0.03065
1-0507-003 F 14 c.3940G>A; p.Ala1314Thr (19) Benign Maternal ASD − 0.05507
7-0167-003 M 4 c.7499A>C; p.His2500Pro (37) Benign Unknown ASD − 0.05984
1-0559-003 M 7.7 c.6148dupA; p.Thr2050fs (31) Pathogenic De novo ASD 0.0437
CHD8-V1 M 10 c.4215G>T; Synonymous (21) VUS Paternal ASD − 0.04478
CHD8-V2 (father of CHD8-V1) M 40 c.4215G>T; Synonymous (21) VUS Not applicable Unaffected − 0.04332
CHD8-V3** M 6.5 c.6649C>T, p.Arg2217* (33) Pathogenic Paternal ASD 0.04616
CHD8-V4 (sibling of CHD8-V3)** M 14 c.6649C>T, p.Arg2217* (33) Pathogenic Paternal ASD 0.03631
DW0013** M 13.5 c.6947delC, p.Pro2316Leufs*39 (35) Likely pathogenic Unknown ASD 0.05183
EX0070-W** M 6.75 c.4327C>T, p.Arg1443Cys (21) VUS Paternal ASD − 0.04131
  1. *Deletion encompassing SH2B1 gene, not overlapping 16p11.2del typical deletion region
  2. **Test case data are from EPIC array, classified using 93 probes overlapping 450K and EPIC arrays from CHD8+/− signature