Table 2. In silico analysis of 13 BRCA1 variants of unknown significance/putative variants affecting splicing.
| NT change (HGVS) | NT change (BIC) | Location | SpliceSiteFinder (0–100) | MaxEntScan (0–12) | NNSplice (0–1) | GeneSplicer (0–15)] | Human Splicing Finder (0–100) | Effect observed in mini-gene assay | RNA change (HGVS) | 5-Tier splicing classificationa |
|---|---|---|---|---|---|---|---|---|---|---|
| c.-19-22_-19-21dupAT | 101−21insAT | Intron 1 | NI ⇒ ⇒ NI | SA: 4.90 ⇒ 4.90 (0%) | NI ⇒ NI | NI ⇒ NI | SD: 71.51 ⇒ 71.51 (0%) | No aberration | r.[=] | Class 2 |
| c.80+1G>A | 199+1G>A | Intron 2 | SD: 91.49 ⇒ NI (−100%) | SD: 10.65 ⇒ NI (−100%) | SD: 1.00 ⇒ NI (−100%) | SD: 1.93 ⇒ NI (−100%) | SD: 95.25 ⇒ NI (−100%) | Skipping of exon 2 | r.[ −19_80del] | Class 5 |
| c.132C>T | 251C>T | Exon 3 | SD: 87.86 ⇒ 83.74 (−4.7%) | SD: 10.08 ⇒ 8.07 (−20.0%) | SD: 0.89 ⇒ 0.70 (−21.9%) | SD: 2.61 ⇒ NI (−100%) | SD: 89.42 ⇒ 87.44 (−2.2%) | Use of cryptic splice site in exon 3 | r.[131-134del] | Class 5 |
| c.213−1G>A | 332−1G>A | Intron 5 | SA: 85.51 ⇒ NI (−100%) | SA: 4.84 ⇒ NI (−100%) | NI ⇒ NI | NI ⇒ NI | SA: 89.39 ⇒ NI (−100%) | Use of cryptic splice site in intron 5 | r.[212_213ins213-59_213-1; 213-1g>a] | Class 5 |
| c.302−15C>G | 421-15C>G | Intron 6 | SD: 91.50 ⇒ 91.50 (0%) | SA: 11.68 ⇒ 10.21 (−12.6%) | SA: 0.99 ⇒ 0.98 (−0.5%) | SA: 8.44 ⇒ 6.46 (−23.4%) | SA: 87.76 ⇒ 87.76 (0%) | No aberration | r.[=] | Class 2 |
| c.547+14delG | 666+14delG | Intron 8 | SD: 81.89 ⇒ 81.89 (0%) | SD: 9.08 ⇒ 9.08 (0%) | SD: 0.93 ⇒ 0.93 (0%) | SD: 1.08 ⇒ 0.74 (−31.4%) | SD: 91.23 ⇒ 91.23 (0%) | No aberration | r.[=] | Class 2 |
| c.670+1delG | 789+1delG | Intron 10 | SD: 73.32 ⇒ NI (−100%) | SD: 5.98 ⇒ NI (−100%) | SD: 0.89 ⇒ NI (−100%) | NI ⇒ NI | SD: 79.94 ⇒ NI (−100%) | Use of cryptic splice site in exon 10 | r.[670del] | Class 4 |
| c.670+16G>A | 789+16G>A | Intron 10 | SD: 73.32 ⇒ 73.32 (0%) | SD: 5.98 ⇒ 5.98 (0%) | SD: 0.89 ⇒ 0.89 (0%) | NI ⇒ NI | SD: 79.94 ⇒ 79.94 (0%) | Increased inclusion of exon 10 | Class 3 | |
| c.4185+1G>A | 4304+1G>A | Intron 12 | SD: 82.52 ⇒ NI (−100%) | SD: 8.59 ⇒ NI (−100%) | SD: 0.95 ⇒ NI (−100%) | SD: 5.17 ⇒ NI (−100%) | SD: 85.50 ⇒ NI (−100%) | Skipping of exon 12 | r.[4097_4185del] | Class 5 |
| c.4676−20A>G | 4795−20A>G | Intron 15 | SA: 84.71 ⇒ 84.71 (0%) | SA: 10.20 ⇒ 9.30 (−8.8%) | SA: 0.92 ⇒ 0.89 (−3.3%) | SA: 9.08 ⇒ 7.09 (−21.9%) | SA: 89.79 ⇒ 89.79 (0%) | No aberration | r.[=] | Class 2 |
| c.4987-21G>T | 5106−21G>T | Intron 16 | SA: 84.55 ⇒ 84.55 (0%) | SA: 6.69 ⇒ 6.69 (0%) | SA: 0.61 ⇒ 0.74 (+20.9%) | SA: 1.36 ⇒ 1.91 (+40.6%) | SA: 87.03 ⇒ 87.03 (0%) | No aberration | r.[=] | Class 2 |
| c.5075-1G>C | 5194−1G>C | Intron 17 | SA: 92.62 ⇒ NI (−100%) | SA: 8.96 ⇒ NI (−100%) | SA: 0.89 ⇒ NI (−100%) | SA: 8.21 ⇒ NI (−100%) | SA: 91.29 ⇒ NI (−100%) | Skipping of exon 18 | r.[5075_5152del] | Class 5 |
| c.5278−14C>G | 5397−14C>G | Intron 20 | SA: 90.05 ⇒ 90.05 (0%) | SA: 13.07 ⇒ 12.43 (−4.9%) | SA: 0.99 ⇒ 0.99 (0%) | SA: 14.41 ⇒ 12.59 (−12.7%) | SA: 93.64 ⇒ 93.64 (0%) | No aberration | r.[=] | Class 2 |
Abbreviations: NI, not identified; SA, splice acceptor; SD, splice donor; wt, wild type.
The thresholds represent score predicted for wt sequence/score predicted for variant sequence. Scores indicate the values for SD or SA sites, respectively.
Changes relative to wild-type sequences are indicated in % (bold if >10%).