The Doctor handed it back to her " Because my sister had one like this, and well stuff that guy said on the phone, But if hes who I think he is. you might be in danger, but we need to do some DNA tests and maybe a few other things." He was speaking softly. "I assumed my sister had died, but maybe she just lost her memories and is you. I'm not full sure, so we do need to check, "
He was scared of finding out the truth, what if he was wrong. "Jack have you ever checked how many hearts she has? Time Lords have two, if she is a time lord she would have two, even if shes not my sister, if she has two hearts she would be a time lord."
He knew her knowing the truth would be safer for her. He didn't want to upset her too much. But he knew that she was wanted, He wasn't sure if she had made herself human or only just lost the memories and still was time lord.