| Genomic variant |
Location |
Motif |
Reference
score/motif
(WT) |
Variant
score/motif |
Effect/variation (%) |
| rs17049422* (c.217-141G/A) |
Intron 3 |
Acceptor site1 |
5.46 |
5.13 |
-6.04 |
| Branch point site2 |
73.64 |
66.75 |
-9.36 |
| SC352 |
81.75 |
84.33 |
3.16 |
| SRp402 |
|
78.44 |
New site |
| Enhancer EIE3 |
present |
|
Site broken |
| Enhancer 9G82 |
|
65.57 |
New site |
| Enhancer Tra2-b2 |
|
85.42 |
New site |
| rs79588315* (c.217-11T/C) |
Intron 3 |
Acceptor site2 |
78.59 |
76.74 |
-2.35 |
|
Acceptor site1 |
3.01 |
1.83 |
-39.2 |
|
Enhancer EIE3 |
|
present |
New site |
|
Silencer IIE3 |
present |
|
Site broken |
| rs115418265 |
Intron 4 |
Enhancer EIE3 |
|
present |
New site |
| Silencer Motif 34 |
67.6 |
|
Site broken |
| Silencer IIE3 |
|
present |
New site |
| rs7594702 |
Intron 4 |
Donor site2 |
68.02 |
67.78 |
-0.35 |
| SF2/ASF (IgM-BRCA1)2 |
74.31 |
75.19 |
1.19 |
| SF2/ASF2 |
82.59 |
75.19 |
-8.96 |
| Silencer Motif 24 |
70.15 |
|
Site broken |
| Silencer Motif 24 |
60.23 |
|
Site broken |
| Silencer IIE3 |
present |
|
Site broken |
| rs73944840 |
Intron 4 |
SC352 |
83.77 |
80.27 |
-4.18 |
| SRp402 |
80.12 |
82.28 |
2.69 |
| SF2/ASF (IgM-BRCA1)2 |
74.08 |
82.28 |
11.07 |
| Silencer Motif 34 |
|
61.51 |
New site |
| Silencer Motif 34 |
62.08 |
|
Site broken |
| rs28588526 |
Intron 4 |
Donor site2 |
50.37 |
77.18 |
53.3 |
| SC352 |
|
75.85 |
New site |
| SRp402 |
|
83.71 |
New site |
| Enhancer EIE3 |
present |
|
Site broken |
| Silencer IIE3 |
|
present |
New site |
| rs28391566 |
Intron 4 |
SF2/ASF (IgM-BRCA1)2 |
|
71.15 |
New site |
| Enhancer EIE3 |
|
present |
New site |
| Silencer hnRNP A12 |
74.53 |
|
Site broken |
*Variant genotyped in our breast cancer cohort
EIE: exon-identity elements
IIE: Intron-identity elements
1Yeo & Burge, 2004, j Comput Biol 11:377
2 Based on Human Splicing Finder matrices
3 Zhang C et al 2008, PNAS 105:5797
4 Sironi M et al 2004, Nucleic acids research 32:1783 |
