Verification code when adding new telephone number
You can follow verification message method. When a user add/updates a phone number, you can send a unique random number which he must enter to verify his phone number.

Create a table that will contain three columns phone-number, unix time stamp and the verfication-code. When a user adds a phone number, create and store the random number. When the user inputs the verfication-code(random number), look it up in the database and then authenticate the user. Once he is authenticated, you can remove the entry from the database. 

If you mention that verification code is valid only for 5 mins, then you can run a cron job to clear the database entries which are older than 5 mins.