1. I can tell Jasmine must have had a difficult childhood,although I don’t know exactly what she “has” gone through .
2. I can tell Jasmine must have had a difficult childhood,although I don’t know exactly what she “had” gone through .

Whats the difference?are they all correct?

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@aries0402 #1 is correct. In #1, you are speaking about Jasmine in the present tense, and “has” refers to events she has already experienced.
In #2, you would need to be speaking in the past tense for “had” to be correct, as in “although I didn’t know exactly what she had gone through.”
To make #1 sound a little more natural, you can say “what she has been through.”