You do know that the TSA agent also handles paper boarding passes and your identification while spreading those heebee jeebee germs, right?
True true, but I use my phone 24/7 - my paper boarding pass I usually fold up, put in my bag, and discard. But yeah, you're right - I'm not a super paranoid germaphobe but I do know most people's phones are loaded with nice amounts of bacteria.
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You don't hand the TSA guy your phone. You place it face down over the scanner yourself.
And it doesn't touch the screen, it will scan from several inches above it.
This is true - however, quite a few people were unable to get it to beep on their own because they'd place their phone face down on the glass. So the TSA/gate representative would take the phone, lift it up a good 2-3cm then it would beep. I have a big case on mine so the glass doesn't touch, but I saw the mistake people made, and was able to make mine beep --- the barcode is on the lower part of the phone, so that's what needs to be placed in the middle.
But yeah, they happily let you handle your own phone as long as you can get it to beep.