Table 8 Tier1 and Tier2 variants in HCC and Non-HCC samples (GRCH37) all heterozygous, population frequency < 0.1
From: Genomic landscape of hepatocellular carcinoma in Egyptian patients by whole exome sequencing
| Â | Variant | Phred | Position | Sequence ontology/ VAF | ACMG category | HCC LT/Non-HCC LTN (VAF) |
|---|---|---|---|---|---|---|
1 | TP53 c.422G > A NM_000546.6 | 101 | chr17 7,578,508 | Missense | Tier1 | LT19 (22.95%) |
2 | CDKN2A c.95 T > A NM_000077.5 | 25 | chr9 21,974,732 | Missense | Tier1 | LT14 (7.14%) |
3 | MSH2 c.56del NM_000251.3 | 37.6 | chr2 47,630,385 | Frameshift | Tier2 | LT13(18.18%) |
4 | KMT2D c.8713_8715delinsG NM_003482.4 | 20.4 | chr12 49,432,424 | Frameshift | Tier2 HP | LT11N (4.76%) |
5 | KMT2D c.5135_5136del NM_003482.4 | 17.3 | chr12 4,943,803 | Frameshift | Tier2 HP | LT11N (3.86%) |
6 | KMT2D c.5135del NM_003482.4 | 27.6 | chr12 49,438,036 | Frameshift | Tier2 HP | LT17N (10.29%) |
7 | ATM c.6348-2A > G NM_000051.4 | 23 | chr11 108,190,679 | Splice site | Tier1 | LT20N (4.11%) |
8 | KIT c.1621A > C p.Met541Leu NM_000222.3 | 119 | chr4: 55,593,464 | Missense | Tier2 | LT11, 18,19 (22%, 43%, 52%) |
9 | KMT2D c.8455C > T NM_003482.4 | 8.7 | Chr12 49,432,684 | Stop_gained | Tier2 | LT7 (3.33%) |
10 | KMT2D c.3553C > T NM_003482.4 | 11.8 | Chr12 49,443,818 | Stop_gained | Tier2 | LT7 (4.29%) |
11 | NOTCH1 c.1773C > A NM_017617.5 | 8.9 | Chr9 139,410,065 | Stop_gained | Tier1 | LT8N (3.23%) |
12 | KMT2C c.1084_1085insC NM_170606.3 | 8.3 | chr7-151,962,222 | Frameshift | Tier2 | LT10 (3.28%) |
13 | PIK3CA c.1325_1326insG NM_006218.4 | 8.9 | Chr3 178,928,048 | Frameshift | Tier1 | LT11 (3.57%) |
14 | KMT2D c.9279_9280insG NM_003482.4 | 7.7 | Chr12 49,431,859 | Frameshift | Tier2 | LT11N (2.2%) |
15 | KIT c.1149dup NM_000222.3 | 8.5 | Chr4 55,575,619 | Frameshift | Tier1 | LT11N (4.76%) |
16 | SMARCA4 c.3392del NM_003072.5 | 17.7 | Chr 19 11,141,415 | Frameshift | Tier2 | LT13 (7.73%) |
17 | KMT2D c.15838_15839insC NM_003482.4 | 7.7 | Chr12 49,418,675 | Frameshift | Tier2 | LT14 (1.75%) |
18 | SMARCA4 c.1834_1835insG NM_003072.5 | 7 | Chr19 11,113,727 | Frameshift | Tier2 | LT14 (1.85%) |
19 | NOTCH1 c.3763_3764insC NM_017617.5 | 7.4 | Chr9 139,401,305 | Frameshift | Tier1 | LT17 (2.82%) |
20 | ATM c.5870_5871insC NM_000051.4 | 8 | Chr11 108,180,994 | Frameshift | Tier1 | LT18N (3.17%) |
21 | PTEN c.812 T > C NM_000314.8 | 7.3 | chr10 89,720,661 | Missense | Tier2 | LT18N (2.78%) |
22 | MSH2 c.577C > T NM_000251.3 | 7.3 | Chr2 47,637,443 | Stop_gained | Tier2 | LT19 (2.78%) |
23 | PTCH1 c.1963C > T NM_000264.5 | 8.5 | Chr9 98,231,320 | Stop-gained | Tier1 | LT7N (3.23%) |