Table 1 Copy number variants (CNVs) used to test the three different classification systems
From: Adapting ACMG/AMP sequence variant classification guidelines for single-gene copy number variants
# | Type (CN) ISCN | Gene | Inheritance | Variant description | Hypothetical clinical information |
|---|---|---|---|---|---|
1 | Del (×1) | ACTN2 | AD | Intragenic, gene lacks established LOF mechanism | Cardiomyopathy |
arr[GRCh37] 1q43(236900784 × 2, 236902335_236903093 × 1, 236905916 × 2) | |||||
2 | Del (×1) | CLN3 | AR | Intragenic, published20 | History of seizures |
arr[GRCh37] 16p11.2(28497100 × 2, 28497674_28498122 × 1, 28498500 × 2) | |||||
3 | Del (×0) | DMD | XL | Predicted in-frame, published, exons 48-4921 | Male with dilated cardiomyopathy |
arr[GRCh37] Xp21.1(31838419 × 1, 31854531_31916869 × 0, 31947426 × 1) | |||||
4 | Del (×1) | SCN1A | AD | Predicted in-frame, exons 12–16, similar published del22 | No clinical information provided |
arr[GRCh37] 2q24.3(166872652 × 2, 166892537_166898952 × 1, 166898963 × 2) | |||||
5 | Del (×1) | BRCA1 | AD | Involving last exon and stop codon, published23 | Family history of breast cancer |
arr[GRCh37] 17q21.31(41184507 × 2, 41197252_41197790 × 1, 41197794 × 2) | |||||
6 | Del (×1) | MECP2 | XL | Involving part of the last exon (excluding stop codon) | Female with epilepsy and DD |
arr[GRCh37] Xq28(153295905 × 2, 153295993_153296345 × 1, 153296809 × 2) | |||||
7 | Del (×0) | DMD | XL | Deeply intronic, ~half of one intron | 10-year-old male with ASD |
arr[GRCh37] Xp21.1(32878477 × 1, 32895663_32967974 × 0, 32984401 × 1) | |||||
8 | Dup (×3) | DMD | XL | Involving 3’ end of gene, published24 | Female with DD |
arr[GRCh37] Xp21.2(31107479 × 2, 31138211_31241488 × 3, 31241306 × 2) | |||||
9 | Dup (×2) | DMD | XL | Presumed intragenic, exon 42, published25 | Male with proximal weakness, elevated CK, and phenotype consistent with dystrophinopathy;26 mother negative (maternity confirmed) |
arr[GRCh37] Xp21.1(32306090 × 1, 32318495_32328670 × 2, 32339798 × 1) | |||||
10 | Dup (×3) | TSC2 | AD | Presumed intragenic, 5 exons | Skin, brain, kidney, heart findings consistent with TSC;26 family studies: affected mother and affected sibling positive, two unaffected siblings negative |
arr[GRCh37] 16p13.3(2111829 × 2, 2111948_2120422 × 3, 2120766 × 2) | |||||
11 | Del (×1) | CLN3 | AR | Includes entire gene | Seizures, no other CLN3 variant detected |
arr[GRCh37] 16p11.2(28485855 × 2, 28488533_28503629 × 1, 28505126 × 2) | |||||
12 | Del (×1) | PRDM16 | AD | Includes entire gene | Cardiomyopathy |
arr[GRCh37] 1p36.32(2984478 × 2, 2985600_3350610 × 1, 3365000 × 2) | |||||
