If you are cracking an entrance, then the 12th marks matters only for the eligibility purpose. For example, in NEET there is a minimum marks of 50% in 12th. The 12th marks only matters for eligibility. Once you are above 50%, you are eligible for the examination & the admission will be on the basis of the entrance rank.

This applies for all the entrances conducted.

I hope this answer provides you some insight. Wish you a great eve!