Mac makes beeping sound every five minutes without pop up notification. Origin unknown
Thank you all for commenting. 

Finally, I managed to identify the culprit. The sound (beeping) was actually an alert by the app (Effortless). (I quit app by app, when the sound suddenly stopped). The alert got probably turned on by a recent update, as I don't remember turning it on/off. 

Here is the preference I needed to turn on to mute the sound.