Regarding the ovaries and uterus (still assuming girl), the omphalocele will most likely not contain the ovaries and uterus.
If this is a chromosomal abnormality, our chances of this continuing are quite low, according to the genetic counselor.
Statistics: 25% of omphaloceles are genetically related. 2/3 of omphaloceles are either genetically related or have other problems associated with it. This means that there is a 1/3 chance that the omphalocele is the only problem we're dealing with. That's a lower statistic than we want, but the good news is most of the "other" non-genetic problems deal with the heart, which we are almost certain is good.
The amniocentesis went well. It did not take as long as we thought either. We ordered two tests. There is one test that is about 100% accurate that will take about 2-3 weeks to get results back. The second test is not quite 100% accurate but is still extremely accurate that we will receive in a couple of days. When we get that result we will post it.
Thanks for the thoughts and prayers.