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I think you should reach out to admissions counselors at each of the schools you want to apply to. I would schedule a meeting with them, and send them a copy of your transcript and resume to review. They can then suggest a masters program or tell you to apply now and they will be relatively honest about your competitiveness. This will not only give you some insider-info to each of the schools, but also shows that you care!

My personal advice is if you can afford to apply, there is no harm in applying now. However, I would make sure that your LOR's are perfect AND that your explanation statement is used very strategically. Make sure your personal statement is not a retelling of the experience you have at various clinics, but be raw and human - show your personality.

I think you have a lot of characteristics that make you a unique applicant, so play on those. They won't be enough to "ignore" your GPA, but if you can get an interview, who knows what could happen! If I were you, I would expect to need to apply for a few cycles (and that is okay! If you are okay with it).

Also, I'm a first-time applicant - so take what I say lightly.
 
The only downside I really see to applying now is money. Some schools may be willing to overlook your GPA in favor of your experience, as long as you meet their cutoffs (confirm that you do, because it would be a waste to apply if you don't). You can reach out to the admissions committee at the schools you're interested in to make sure that your application won't just be tossed out when they see those stats.

I think in your shoes I would go ahead and apply and see where it gets you while also looking towards a plan for rejection. If you can't feasibly retake pre-reqs, doing a master's is a good idea to show that your academics have improved. You can work on getting that lined up too, so you're not just adding unnecessary gap time.
 
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