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Pain near belly button related to ovarian cyst?

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I've been seeing a fertility doctor for a few months and during my first ultrasound they found a large cyst in my right ovary. It got smaller and has not changed in size the last 3 months (it's about 3 cm) so the doctor said it is probably benign. My question is about an intermittent pain I have had in my lower right abdomen close to my pelvic bone an inch or so to the right of my belly button. It has been coming and going for a couple months. I will sometimes go days without feeling it but sometimes it will come and go several times in one day. It's kind of a dull but occasionally sharp pain but its not severe. It seems like it's too high and to the right to be coming from my ovary but could this be caused by the cyst? Or is it something else like an intestinal problem? I asked the doctor but she didn't seem concerned and said it might be that fluid escaped from my ovary when the cyst got smaller but it hasn't changed size recently and I still get the pain. What might be going on? FYI I am 28 and have never been pregnant and my cycles have always been normal. Thanks
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