It might be comforting to you that the rights granted in the Constitution come from God but it really defies logic. The Constitution had to be ratified to become law and has had parts added and deleted since its inception. I doubt if God left some rights out or changed his mind.
Please, tell me - where in the Consatitution does it ever say that the U.S. government grants a right?
Also - why does the Constitution say that rights "shall not be infringed" if it's really the Constitution that grants them in the first place.
They argued over the wording that would best state what rights they thought they needed to explicitly protect.
Why have a 9th amendment that says "The enumeration in the Constitution, of certain rights, shall not be construed to deny or disparage others retained by the people." if the Constitution is the document that grants rights?
Your statement is what defies logic, not the philosophy of natural rights as embodied in the DoI and the BoR.
The Constitution does not grant rights, it is a limitation on the powers of government. Amendment 9 states:
"The enumeration in the Constitution of certain rights shall not be construed to deny or disparage others retained by the people."
The Constitution doesn't tell the people what rights they have, it tells the government what it's limitations are, including some of the important rights of the people that it cannot infringe.