Table 2 Detected pathogenic and likely pathogenic single-nucleotide variants, small indels, and copy number alterations
Index patient identifier | Gene (transcript GRCh37/hg19) | Variant type | dbSNP | Exons/total no. of exons | cDNA change | Predicted amino acid change | Aberration array CGH | ACMG class | Previously reporteda |
|---|---|---|---|---|---|---|---|---|---|
7 | PALB2 (NM_024675.3) | Frameshift | rs515726124 | 4/13 | c.509_510delGA | p.(Arg170Ilefs*14) | Â | 5 | Yes |
30 | RUNX1 (NM_001754.4) | Splice donor | rs375131372 | 3/8 | c.97+1G>A | Â | Â | 4 | No |
32 | ATM (NM_000051.3) | Deletion |  | 62–63/63 |  |  | arr [GRCh37]11q22.3 (108233779_108240057)×1 | 5 | Yes |
40 | ATM (NM_000051.3) | Nonsense | Â | 61/63 | c.8793T>A | p.(Cys2931*) | Â | 5 | Yes |
CHEK2 (NM_007194.3) | Deletion |  | 9–10/15 |  |  | arr [GRCh37]22q12.1 (29092709_29097723)×1 | 5 | Yes | |
58 | CDKN2A (NM_058195.3) | Nonsense | Â | 2/3 | c.292C>T | p.(Arg98*) | Â | 4 | No |
RECQL4 (NM_004260.3) | Splice donor | Â | 7/21 | c.1390+1G>C | Â | Â | 4 | No | |
59 | WRN (NM_000553.4) | Deletion |  | 15–16/35 |  |  | arr [GRCh37]8p12 (30948138_30949422)×1 | 4 | No |
60 | ATM (NM_000051.3) | Nonsense | rs587779852 | 40/63 | c.5932G>T | p.(Glu1978*) | Â | 5 | Yes |
65 | FANCI (NM_001113378.1) | Nonsense | rs121918164 | 37/38 | c.3853C>T | p.(Arg1285*) | Â | 5 | Yes |
PMS2 (NM_000535.5) | Deletion |  | 3–8/15 |  |  | arr [GRCh37]7p22.1 (6035238_6042593)×1 | 5 | No | |
76 | PALB2 (NM_024675.3) | Frameshift | rs180177143 | 3/13 | c.172_175delTTGT | p.(Gln60Argfs*7) | Â | 5 | Yes |
79 | RECQL4 (NM_004260.3) | Missense and splice region | rs186739072 | 16/22 | c.2755G>A | p.(Ala919Thr) | Â | 4 | No |