Here is what the AFI says:
A188.8.131.52.6. Any significant congenital abnormalities of the heart and vessels, unless corrected by surgery without residuals or complications. A minimum recovery period of 6 months following surgery is mandatory before waiver is considered together with repeat studies including invasive testing as applicable, demonstrating functional correction.
Uncomplicated dextrocardia and minor atrial and ventricular septal defects may be acceptable without surgical correction.
So, yours could very well be accepted, but the Medical Evaluation Board will determine that. Good luck.
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