If you go by canon, then Prime Base doesn't house any frozen dependents.
But we do have the secondary command base, which would be a logical candidate. In my campaign, I have a frozen scientific research base as well as the various regional bases which can also house frozen family members.
It's an interesting question (and a welcome change from the "all 32 members of my family died in a bizarre house fire, causing me to join the military and graduate Marine Force Recon, Special Forces and Delta Force" backstory).