You can use del() or you can re-create the list by filtering it:
>>> phone = {"first":100,"second":200,"third":[10,12,5,38],"fourth":400}
>>> phone['third'] = [x for x in phone['third'] if x not in (12,5)]
>>> phone
{'second': 200, 'fourth': 400, 'third': [10, 38], 'first': 100}