After reviewing the two sources linked to by the CDC (a Rand report on the impacts of comorbid chronic conditions and a brief breakdown of US health expenditures) the exact methodology behind the 90% figure is not at all clear to me.
What you are asking for would be a considerably more complex calculation. The most directly relevant study I'm seeing so far is an old one, "An Epidemiological Model for Health Policy Analysis" G. E. Alan Dever (1976). In the following table (p. 462), the author attempts to break down how four different causes (one of which is "Human biology") contribute to mortality from various kinds of diseases:
Notice that even for "congenital abnormalities", the contribution of human biology is only weighted at 79%. The rest is accounted for by the health care system, lifestyle and environment. The average contribution of human biology for all causes of deaths is estimated at 27%. This is not directly relevant to the question, but I think it illustrates how the author is thinking about the contribution of different factors to disease.
Taking in to account the relative prevalence of different diseases, the author uses these estimates to further project that about 7% of federal healthcare expendatures are the direct result of human biology, independent of other factors.
There may be more up-to-date studies out there with better methodologies, but I hope this is helpful as an example of how an expert might approach the question.