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Whenever someone asks a stupid nosy question I always look disgusted then say the answer opposite to what they are expecting me to say. So in your situation it would have went like this-
MIL "Are you having an affair?"
ME *Looks utterly shocked and disgusted at the question* "OF COURSE I AM!"
It shuts them up usually.
If someone asks a question I don't want to answer I say "why do you ask?" It's a polite way of saying I think it's weird that they want to know as it's not their business.
My MIL once saw some tablets in my handbag, fished them out and held them up while asking 'are you pregnant?' (In a disgusted tone)
Ah, mother in laws.
Mine is like that I find it trude as its not her business. I just say no one and move on.
I'd just say who it was? Unless it was a call from the doctor or something that I didn't want people knowing about; then I would just say it was my sister or something.
I really don't get what the big deal is. First world problems!