This appears to be a birth defect or a genetic abnormality. It isn't natural for anyone to look that way. It isn't that you're too thin and the collar bone has nothing to cushion it. It looks as if your neck itself is misaligned and was set back too far.
If I were you, I would see if I could find someone locally that could take a look at it and see if this is something that can actually be fixed. It looks like this could cause some pretty severe complications with spine and spinal curvature as you grow older.
Now, I would have said, "Maybe she's just too thin and there's nothing surrounding the bone..." but you have a good body shot there and you look like a good weight for your height to merit the assumption of poor eating habits or even an eating disorder. Sometimes when a girl is too thin they get that boney look at the top and gaining just a little bit of weight can help plump it out enough to look right. This is not your case.
So, I would definitely talk with your doctor about seeing someone in the spinal care range. It already sort-of looks like your head is hunching forward, just slightly, to make up for the misalignment. It could just be the shots or something you were doing during the time the photos were being taken but, to me, it looks uncomfortable. I could only imagine the possible back pain that may actually be accompanied by this now or in the future.
You're a very pretty girl though. Trust me. It doesn't make you ugly or even weird. It's just, when you're looking directly at the issue, a person does think, "That isn't quite right."
It's possible it's just something inherited. It's possible it is a birth defect. It's possible your not weight proportionate at your upper half and for some odd reason there is no fatty tissue around this bone.
I'd talk with a doctor and make sure this isn't going to affect you growing older.
While you're waiting for your doctor's appointment, maybe you should play around with make-up. I mean, heck, if applying make-up just right can create the "ripped abs" affect on your torso then surely it can diminish the appearance of flaws. Go light and try to make things blend in more and look more natural. If you can lighten the shadowed parts then maybe it won't look like it's standing out so much. Of course, I recommend you messing around with covering this up at home rather than winging it at school.
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