Flight Crew Air Transport Pilot (ATP); Flight Crew Instrument; Flight Crew Multiengine
Flight Crew Last 90 Days 90; Flight Crew Total 8200; Flight Crew Type 250
Communication Breakdown; Human-Machine Interface
Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy; Inflight Event / Encounter CFTT / CFIT
Air Traffic Control Issued Advisory / Alert; Air Traffic Control Issued New Clearance; Flight Crew Took Evasive Action
Human Factors
Downloaded filed flight plan from ARINC to our FMS at ZZZ.After picking up our clearance which was different than the filed route; I updated the FMS with the new clearance and waypoints. Somewhere along the rush I mistakenly deleted ZZZ VOR and kept ZZZ1 VOR. So the issue came about on the leg between ZZZZZ and ZZZ1 VOR. ATC issued a terrain alert with an immediate left turn and a climb to FL130. After being told of a possible pilot deviation I looked at the route and realized my mistake.The aircraft EGPWS never indicated a terrain issues and after looking at the route from ZZZZZ to ZZZ1 at FL120 on ForeFlight Map we were above the terrain and therefore never should have heard the EGPWS as we did not.Weather conditions at time; we were in between broken layers with good visibility in front of us.
Challenger 300 flight crew reported accidentally deleting a waypoint from the FMS resulting in an altitude deviation and low altitude alert.