I go to a Catholic private high school and one of the requirements at the school is to have a mandatory religion class every year. In this class, we receive a grade and it is impossible to receive anything above a 4.0 for the class because obviously, honors or AP religion would be ridiculous. When colleges look at my transcript will they cut out the class themselves or will they just look at my UC GPA which has the class cut.
Religion is not considered an a-g course requirement for the UC’s. They will look at all your grades, but only the a-g courses count for the UC GPA. You also only self report a-g courses on the UC application.
@Gumbymom thank you. I was wondering what about private schools?
If your high school is listed at https://hs-articulation.ucop.edu/agcourselist#/list/search/institution (includes California public and private high schools and some distance learning high school programs), then you can find out what courses there fit into each a-g category for UC and CSU purposes.
Private schools will focus on your academic courses but if you are applying to a Religious based private, they may take a look at your Religion grades. Not really sure about if this would have an impact. You could check each school’s website to see what is considered in their admission review. You could also look at the common dataset for each school which spells out what admissions looks for in an applicant.
Most private colleges (and public colleges, for that matter) will either look at your UW GPA, or will reweight (or in the case of the UC’s, tell you to reweight) according to its own parameters. There are 30,000 HS’s in the US, and their weighting systems are all over the board, so colleges try to look at transcripts and compare apples to apples as best they can.
In terms of what classes any particular college will include in the GPA calculation, some colleges will include all academic classes, including art, music, and religion. Some will just include core classes (English, math, science, history/social studies, foreign languages). What any particular college chooses to include, and how they weight the courses (if at all) is out of your control, so don’t stress about it.
Regardless, all colleges know that some HS’s have requirements that other HS’s may not. They all know that Catholic HS students all have to take 4 years of religion. Again, it is what it is. Many students from Catholic HS’s go to top colleges too. 
Good luck.
thanks for the responses @skieurope @Gumbymom
@skieurope gave a much better explanation than I could. ^^^^