But that is a meaningless comparison. The doctor should be comparing this additional risk, to the benefit of the scan.
The "natural" risk of developing cancer is totally irrelevant to the cost-benefit analysis.
I wonder though if there should be a cutoff somewhere, below which you stop caring? I used background cancer rates as an anchor to judge if the cutoff has been reached, without getting specific about benefits of treatment in each particular case. Would you suggest another cutoff level that is broadly applicable?
So if you are certain that the benefit of the scan is, no matter what the particular case, going to be worth much more than a 1/1000 chance of getting cancer, then that is a reason to ignore the risk.
If I want to know whether to do a CT scan, the only relevant fact is the increase in probability (in an absolute sense) of cancer that it causes.
It seems like either you, or the entire field of medicine, is obfuscating this basic fact using some field-specific concepts.
EDIT: It seems like you are referring to relative risk (http://en.wikipedia.org/wiki/Relative_risk). But as I said, there is no reason that relative risk should be considered in this case.