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DoubleDach

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The only potential issues I see are lack of recent clinical experience and lower than average stats. But even with that it's certainly surprising you didn't get more attention. Did you have people look over your essays?
 
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With an undergrad GPA of <3.5, you are probably getting caught in the first pass filter and nobody even gets a look at the rest of your application.

I'm not totally sure how to remedy this. I think postbac programs will count toward your undergrad GPA but if you already did all your science prereqs I'm not sure you can take that route.

In your shoes I might try to think about alternative paths to the career you want, including starting with a straight PhD, for which you would be a much stronger candidate and could very reasonably expect to enter a great school in the geographic area of your choice, or else a straight MD (but you might need to consider casting a wider net in that case).
 
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3 IIs is great- it could have been luck of the draw that it didn’t work out. I would definitely encourage you to apply again MD-PhD. Don’t consider alternative paths just yet- imo. Also potentially there is room for improvement for interviewing.
 
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