First the good news: Admission officials are accustomed to taking a “mix-and-match" approach to evaluating candidates. They often see applications from students who have moved from one high school to another — or even from one country to another — so grading systems, course offerings, etc. can seem out of sync. The admission folks certainly won't view your course selections at your new school as showing a step back in rigor if the more challenging classes simply weren't available.
The bad news, however, is that — if your current school combines your old transcript with your new one -- you may lose some GPA points. For example, let's say that you took three AP classes at your previous school and earned a B (3.0) in each of them. But, because that school did weight grades, those B's might have be computed into your GPA as A's (4.0). But, then, since your new school doesn't weight grades, your GPA could be recalculated using a 3.0 for your AP class B's. And if that's the case, you'll see a dip in your cumulative GPA.
So your next step — if you haven't done so already — is to find out exactly what information colleges are going to receive from your new school. Will this school take away the weighted GPA points you earned at your last school or will it stick with the final grades that appear on your transcript with the weighting included? And will your new school compute a combined GPA for you -- meshing old grades with the upcoming ones — or will two separate transcripts be maintained ... one from your previous school with weighted grades and one from your present school without them ... with a separate GPA on each one? Policies on transfer students vary from high school to high school so it's impossible for “The Dean" to know what to expect from yours.
In any case, you can help admission officials (and yourself!) by writing a paragraph in the “Additional Information" section of your applications explaining your move, the inconsistencies in grading and the more limited AP selection at your new school. If the transcripts are merged and your GPA drops because you've lost the extra weighted points on your AP classes which your last high school had awarded, you can include this, too. (It's very possible that your counselor will provide this explanation in your School Report, but if you're not 100 percent certain that it's been done — and clearly — then do it yourself.)
Note, however, that — just because your current school doesn't offer as many AP classes as your old one did — it's not necessarily less rigorous. Some high schools claim that all of their classes are extremely challenging and they don't need an “Honors" or “AP" label to prove it. So if you feel that your current school provides less opportunity for demanding classes than your other school did, you should discuss this in your “Additional Information" explanation. But if you find that your new classes are very tough yet simply lack the AP label, you should point this out instead.
Make sure that your explanation doesn't sound whiny. The tone should suggest, “I want to save you some confusion as you wrangle with two different school profiles" rather than “I got screwed!"
Bottom Line: You need not worry about being penalized for transferring to a less challenging high school. Admission officers are adept at making apples versus oranges comparisons. But by providing a succinct synopsis of the differences between your two schools, you will save them some legwork, which will surely be appreciated.
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