Hi @tomerk,
I believe you misplaced the corresponding CPU pin names to the GPIO 13 pins in the document you attached. As seen on "Table 11-1. Muxing Options" of the Reference Manual, GPIO13_IO00 corresponds to the WAKEUP pin, not GPIO_SNVS_03. additionally:
GPIO13_IO01 corresponds to PMIC_ON_REQ
GPIO13_IO02 to PMIC_STBY_REQ
GPIO13_IO03 to GPIO_SNVS_00
GPIO13_IO04 to GPIO_SNVS_01
and so on...
Finally GPIO13_IO12 corresponds to GPIO_SNVS_09. There is no GPIO_SNVS_10, GPIO_SNVS_11 or GPIO_SNVS_12. I believe you got the signals mixed up.
You can also refer to example code "igpio_input_interrupt" from the SDK, as it also uses GPIO13.
BR,
Edwin.