Table 2 Summary of SNVs observed in NF2, TRAF7, SMO, AKT1, and KLF4 genes
Chromosome | Gene | Position | Vartype/Effect | Genotype | Variant | Biotype | EXAC_AC | EXAC_AN | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
Blood | Tumor | Early | Late | ||||||||
chr22 | NF2 | 30038152 | SNP/intron_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.364-39A > C | Protein_coding | 22478 | 121410 |
|  |  |  | SNP/intron_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.115-39A > C | Protein_coding | 22,478 | 121410 |
|  |  |  | SNP/intron_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.238-39A > C, | Protein_coding | 22,478 | 121410 |
|  |  |  | SNP/intron_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.241-39A > C | Protein_coding | 22,478 | 121410 |
|  |  |  | DEL/intron_variant | 0/1 | 0/1 | 0/1 | 0/2 | c.599 + 56delT | Protein_coding | . | . |
|  |  |  | DEL/intron_variant | 0/1 | 0/1 | 0/1 | 0/2 | c.350 + 56delT | Protein_coding | . | . |
|  |  |  | DEL/intron_variant | 0/1 | 0/1 | 0/1 | 0/2 | c.473 + 56delT | Protein_coding | . | . |
|  |  |  | DEL/intron_variant | 0/1 | 0/1 | 0/1 | 0/2 | c.476 + 56delT | Protein_coding | . | . |
|  |  |  | DEL/intron_variant | 0/1 | 0/1 | 0/1 | 0/2 | c.447 + 13447delT | Protein_coding | . | . |
chr16 | TRAF7 | 2201270 | SNP/upstream_gene_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.-12652G > C | Protein_coding | . | . |
|  |  | 2203456 | SNP/upstream_gene_variant | 1/1 | 1/1 | 1/1 | 1/1 | c.-10466T > C | Protein_coding | 120,133 | 121,104 |
|  |  | 2223864 | SNP/intron_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.1135 + 27G > C | Protein_coding | 15,920 | 117,352 |
|  |  | 2223868 | SNP/intron_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.1135 + 31A > C | Protein_coding | 15,557 | 117,050 |
|  |  | 2223872 | SNP/intron_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.1135 + 35T > C | Protein_coding | . | 120,252 |
chr14 | AKT1 | 105258893 | SNP/intron_variant | 1/1 | 1/1 | 1/1 | 1/1 | c.46 + 42T > C | Protein_coding | 99,675 | 121,090 |
chr9 | KLF4 | 110249505 | SNP/intron_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.1100-32G > A | Protein_coding (p.Gly390Gly) | 21,511 | 121,396 |
|  |  |  | SNP/synonymous_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.1170G > A | Protein_coding (p.Gly390Gly) | 21,511 | 121,396 |
chr7 | SMO | 128845018 | SNP/intron_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.538-26C > T | Protein_coding | 96,595 | 121,412 |
|  |  | 128846328 | SNP/synonymous_variant | 0/1 | 0/1 | 0/1 | 0/1 | c.1164G > C | Protein_coding (p.Gly388Gly) | 96,810 | 121,412 |