From: Identification of genetic variants for clinical management of familial colorectal tumors
Selected variants (VAR) | Reference splice site-dedicated analyses | Cryptic splice site-dedicated analyses | ESR-dedicated analyses | Protein-dedicated analyses | ||||||||||||||||||||
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Patient_ID | Genomic position (GRCh37) | Gene | Exon | Nucleotide change (cNomen) | Predicted protein change (pNomen) | Nearest reference | MES scores | SSFL scores | Potential local splice effect | Local MES scores | ∆tESRseq | ∆Hzei | ΔΨ | |||||||||||
splice site | WT | Var | VAR vs WT | WT | Var | VAR vs WT | WT | Var | ||||||||||||||||
Distance | Type | ∆ (%) | ||||||||||||||||||||||
(nt) | (3’ or 5’ss) | Δ (%) | AGVGD | SIFT | MAPP | PolyPhen-2 | MutationTaster | |||||||||||||||||
3222 & 4932 | chr19:15273335 C>T | NOTCH3 | 32 | c.5854G>A | p.V1952M | 39 | 3’ | 11.5 | 11.5 | 0 | 89.2 | 89.2 | 0 | - | - | - | -1.78501 | -11.15 | -0.89 | C15 | Deleterious | bad | probably damaging | disease causing |
3222 |  | POLE | 25 | c.3046G>A | p.V1016M | -15 | 5’ | 9.1 | 9.1 | 0 | 82.5 | 82.5 | 0 | - | - | - | -0.74478 | 1 | -0.43 | C0 | Deleterious | bad | benign | disease causing |
3308 | chr8:90965597 A>T | NBN | 11 | c.1720T>A | p.L574I | -126 | 5’ | 8.0 | 8.0 | 0 | 82.4 | 82.4 | 0 | - | - | - | 1.97427 | 33.38 | 0.18 | C0 | Tolerated | good | benign | polymorphism |
chr12:133219838 C>T | POLE | 35 | c.4523G>A | p.R1508H | -29 | 5’ | 7.9 | 7.9 | 0 | 73.8 | 73.8 | 0 | - | - | - | -0.600279 | -3.17 | -0.08 | C0 | Tolerated | good | benign | disease causing | |
4932 | chr19:1221318 C>A | STK11 | 6 | c.841C>A | p.P281T | -22 | 5’ | 6.0 | 6.0 | 0 | 79.9 | 79.9 | 0 | - | - | - | -0.17437 | 7.7 | -0.72 | C0 | Tolerated | good | benign | disease causing |
5597 | chr5:56177843 C>G | MAP3K1 | 14 | c.2816C>G | p.S939C | 447 | 3’ | 12.0 | 12.0 | 0 | 100.0 | 100.0 | 0 | - | - | - | -0.486881 | -16.1 | 0 | C0 | Deleterious | good | benign | polymorphism |
9876 | chr17: 40729320 C>T | PSMC3IP | 3 | c.136G>A | p.V46M | 1 | 3’ | 12.5 | 11.7 | -6 | 87.5 | 83.6 | -4 | - | - | - | 2.0413 | 74.24 | -0.3 | C0 | Deleterious | - | possibly damaging | disease causing |
9876 & 8913 | chr14:69061228 G>A | RAD51B | 11* | c.1063G>A | p.A355T | 27 | 3’ | 11.8 | 11.8 | 0 | 80.2 | 80.2 | 0 | - | - | - | -1.24035 | -50.64 | - | C0 | Deleterious | - | benign | polymorphism |
12954 | chr1: 45797950_C>T | MUTYH | 10 | c.812G>A | p.R271Q | 33 | 3’ | 9.5 | 9.5 | 0 | 86.8 | 86.8 | 0 | - | - | - | -2.31042 | 0.88 | 0.09 | C35 | Deleterious | bad | possibly damaging | disease causing |
chr17:56787304 G>A | RAD51C | 5 | c.790G>A | p.G264S | -48 | 5’ | 8.6 | 8.6 | 0 | 75.4 | 75.4 | 0 | New Acceptor Site? | 0 | 2.5 | -1.71397 | -59.31 | -0.21 | C0 | Tolerated | good | benign | disease causing | |
13072 | chr17:41234463 G>A | BRCA1 | 12 | c.4315C>T | p.L1439F | -43 | 5’ | 6.6 | 6.6 | 0 | 85.2 | 85.2 | 0 | - | - | - | -0.261141 | 8.83 | -2.67 | C0 | Tolerated | good | benign | polymorphism |
18843 | chr2:48027317 G>A | MSH6 | 4** | c.2195G>A | p.R732Q | -978 | 5’ | 8.9 | 8.9 | 0 | 81.6 | 81.6 | 0 | - | - | - | -0.805417 | -13.15 | 0 | C0 | Tolerated | good | benign | disease causing |
19673 | chr17:63554395 T>C | AXIN2 | 2 | c.344A>G | p.N115S | 460 | 3’ | 11.1 | 11.1 | 0 | 93.3 | 93.3 | 0 | New Acceptor Site? | 11.1 | 7.2 | -0.162849 | -2.19 | -0.05 | C0 | Tolerated | good | benign | disease causing |
21368 | chr5:56155672 A>G | MAP3K1 | 3 | c.764A>G | p.N255S | -71 | 5’ | 7.5 | 7.5 | 0 | 78.5 | 78.5 | 0 | New Acceptor Site? | 4.7 | 8.8 | -1.18661 | 6.7 | -0.04 | C0 | Tolerated | good | benign | polymorphism |
24447 | chr22:29130636 A>G | CHEK2 | 2 | c.74T>C | p.V25A | 80 | 3’ | 1.7 | 1.7 | 0 | 85.5 | 85.5 | 0 | - | - |  | -0.166788 | 36.67 | -0.07 | C0 | Tolerated | good | benign | polymorphism |
11705 | chr11:108160467 G>A | ATM | 29 | c.4375G>A | p.G1459R | -62 | 5’ | 8.9 | 8.9 | 0 | 87.5 | 87.5 | 0 | - | - |  | 0.552026 | -27.26 | -0.09 | C15 | Deleterious | bad | probably damaging | disease causing |
chr2:47672694 C>G | MSH2 | 8 | c.1284C>G | p.H428Q | 8 | 3’ | 10.1 | 10.1 | 0 | 87.3 | 87.3 | 0 | - | - |  | 0.703136 | 22.05 | 0.05 | C0 | Tolerated | good | possibly damaging | disease causing | |
13393 & 25167 | chr:8_90983460 G>A | NBN | 6 | c.643C>T | p.R215W | 59 | 3’ | 6.2 | 6.2 | 0 | 86.8 | 86.8 | 0 | - | - |  | -1.00071 | -16.87 | -0.09 | C0 | Tolerated | good | probably damaging | polymorphism |
14963 | chr16:23647635 C>T | PALB2 | 4** | c.232G>A | p.V78I | 21 | 3’ | 10.0 | 10.0 | 0 | 90.3 | 90.3 | 0 | - | - |  | -0.783039 | -29.17 | 0.8 | C0 | Tolerated | good | benign | polymorphism |
22953 | chr19:15278214 C>G | NOTCH3 | 29 | c.5208G>C | p.E1736D | 9 | 3’ | 7.8 | 7.8 | 0 | 84.2 | 84.2 | 0 | - | - |  | 0.0501789 | -10.44 | 0.22 | C35 | Deleterious | bad | benign | disease causing |
chr2:47630458 A>G | MSH2 | 1* | c.128A>G | p.Y43C | -84 | 5’ | 10.1 | 10.1 | 0 | 90.6 | 90.6 | 0 | New Donor Site? | 0 | 1.2 | 1.50425 | 4.7 | 2.11 | C55 | Deleterious | bad | probably damaging | disease causing | |
chr14:68352648 T>G | RAD51B | 6 | c.515T>G | p.L172W | -58 | 5’ | 9.5 | 9.5 | 0 | 83.7 | 83.7 | 0 | - | - |  | 1.62772 | 67.77 | 1.31 | C0 | Deleterious | bad | possibly damaging | polymorphism | |
24789 | chr5:112175625 C>T | APC | 15* | c.4334C>T | p.T1445I | 2376 | 3’ | 7.5 | 7.5 | 0 | 93.6 | 93.6 | 0 | - | - |  | -1.61023 | -90.13 | - | C0 | Tolerated | good | benign | polymorphism |
chr16:23646617 G>T | PALB2 | 4** | c.1250C>A | p.S417Y | -435 | 5’ | 8.9 | 8.9 | 0 | 87.5 | 87.5 | 0 | - | - |  | -0.551724 | -22.83 | 0.05 | C0 | Deleterious | bad | probably damaging | disease causing | |
8913 | chr2:47601029 G>C | EPCAM | 3 | c.267G>C | p.Q89H | 83 | 3’ | 7.0 | 7.0 | 0 | 90.1 | 90.1 | 0 | - | - |  | -0.40237 | -28.93 | 0 | C0 | Tolerated | bad | possibly damaging | disease causing |