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That is viscera, not yolk sack. Many animals are born with this deformity, and if the hole is smaller (much smaller) it can be closed and the animal can live. I had a corn snake with a much smaller hole, which I was advised to close with super glue, and the animal lived and was even able to successfully breed later in life. However, I think the deformity was much too severe with your animal, and it would not have survived. I think you did the right thing by culling it. Even if you hadn't, it's unlikely the animal would have lived more than a few days.
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