Sorry to hear about the Covid issues you faced academically and you are not alone, but the UC’s are highly competitive and very strict on making sure you complete all the a-g course requirements with passing grades.
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An AP score of 3 or above will fulfill the US History requirement but you are still required to report all grades received.
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If you do not retake the exact same class/semester, then the D in AP USH will not be replaced and will be calculated into your UC GPA unfortunately. You can retake the 1st semester of APUSH on-line but the grade needs to be reported by Nov 30th on the UC Application.
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Although you took 2 semesters of art courses in the same discipline, if they are not the exact same courses you received the F’s in, then they will not be replaced and you have to report all the courses with the corresponding grades. Again, they will be calculated into your UC GPA.
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A regular Biology course does not replace the DE Biology course grade so again you have to report the grades for both these courses.
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If you are OOS, then there are no UC approved Honors courses, only AP/IB and UC transferable DE courses.
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You have to report all a-g courses that are listed on your HS and College/DE transcript and you will be required to send all transcripts if accepted and enroll in any of the UC’s.
The issue for you is that even if you retake the exact same classes, the UC’s will admit on grades from 10-11th so even if these courses are in-progress, there are no grades to report by the application deadline.
Before applying, you should calculate your 3 UC GPA’s to make sure you meet the minimum GPA requirement for OOS or at least be competitive and also make sure you meet all the a-g course requirements.
You will not be automatically rejected unless you do not meet the minimum a-g course requirements or UC capped GPA.