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The prices vendors quote are also, in a sense, pulled out of thin air. There is some floor to the price based on cost to produce and minimum acceptable margin, and volume also plays a role. But, there are many other factors that are subjective. For example, perhaps the part manufacturer is looking to get its first part into Apple, so they knock some more off the price.

While only Apply knows how much an Apple-proprietary processor costs, it is possible to estimate a cost for it based on process technology, die size, pin count, package, etc.