Table 1.
Genomic findings
| Gene | CHR:POS | HGVS cDNA | HGVS protein | Variant type | Predicted effect | Variant allele frequency (Alt/Ref allele read count) | Read depth of variant |
|---|---|---|---|---|---|---|---|
| BRAF | 7:140477836 | NM_004333.4:c.1457_1471del ATGTGACAGCACCTA | NP_004324.2: p.Asn486_ Pro490del | In frame deletion | Activating mutation (Foster et al. 2016) | WGS: 66% (68/35) WES: 64% (77/44) |
WGS: 103× WES: 121× |
| CDKN2A | 9:21971120 | NM_001195132.1:c.238C>T | NP_001182061.1: p.Arg80a | Nonsense | Variant of uncertain significance likely loss of function (Rachakonda et al. 2013; Yarbrough et al. 1999) | WGS: 62% (48/29) WES: 66% (165/84) |
WGS: 77× WES: 249× |
| TP53 | 17:7579380 | NM_000546.5:c.299_306del AGAAAACC | NP_000537: p.Gln100Leufs Ter46 | Frame shift | Variant of uncertain significance likely oncogenic (Chakravarty et al. 2017) | WGS: 56% (42/33) WES: 52% (82/76) |
WGS: 75× WES: 158× |
| SMAD4 | 18q21.2 | NM_005359.5 | NM_005350.1 | Homozygous deletion | Loss of function (Jia et al. 2017) | Copy-number log2(T/N) = −1.624 | WGS (18q mean coverage): 96× |
aTermination (stop) codon (https://www.hgvs.org/mutnomen/standards.html).