Table 4:
BEN/LBEN Variant Test Set and Criteria
| PTEN Variant | Round 1 review –criteria applied | Initial classification | Round 2 review – criteria added following GVWG review, addition of clinical laboratory data | Final EP classification |
|---|---|---|---|---|
| c.−9C>G (NC_000010.10:g.89624218C>G) | BA1 | BEN | BEN | |
| c.−903G>A (NC_000010.10:g.89623323G>A) | BA1 | BEN | BEN | |
| c.−1026C>A (NC_000010.10:g.89623200C>A) | BS1 | VUS | BS2_P, BP5 | LBEN |
| c.−1059C>G (NC_000010.10:g.89623167C>G) | BA1 | BEN | BEN | |
| c.−1311T>C (NC_000010.10:g.89622915T>C) | None | VUS | BA1 | BEN |
| c.18A>G (p.L6=) | BP4, BP7 | LBEN | LBEN | |
| c.75G>A (p.L25=) | BP7 | VUS | VUS | |
| c.132C>T (p.G44=) | BS1, BP7 | LBEN | BS2_P, BP5 | LBEN |
| c.360A>C (p.A120=) | BP4, BP7 | LBEN | LBEN | |
| c.1104T>C (p.D368=) | BS1, BP4, BP7 | LBEN | LBEN | |
| c.79+35C>T (IVS1+35C>T) | BS1, BS3 | BEN | BEN | |
| c.165-13_165-10delGTTT (IVS2-13_IVS2-10delGTTT) | BS1, BP4 | LBEN | LBEN | |
| c.254-39G-T (IVS4-39G>T) | BP4, BP7 | LBEN | LBEN | |
| c.801+23G>A (IVS7+23G>A) | BS1, BP4 | LBEN | LBEN | |
| c.1026+32T>G (IVS8+32T>G) | BA1 | BEN | BEN |