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In general, this means that the lesion is abnormal without being cancerous. However, it has to be used in a clinical context. So if your doctor took a small biopsy of a large spot, there may still be an issue and additional biopsies may be needed. Best thing to do is to talk to the treating dermatologist.
Melanotic hyperplasia means there is an increase in the number of malanocytes (The cells that contain the pigment , melanin). It is not as atypical mole. If the melanocytic hyperplasia extends to the margin, it should be excised, just for safety. It also means you need a full examination of your moles on regular basis, at least oce a year.
Yes, this does mean you have a mildly atypical mole. The fact that it is "junctional" also means that it is quite superficial which is good news. Since it extends to the margins you need to have the remainder of it removed. Depending upon its location, I will frequently do a deeper and wider shave excision to remove what is left which can result in a much better scar than having the area fully excised. I recommend you be treated by a board certified dermatologist to have this option for treatment as well as for careful follow-up of the area. I also recommend returning for total skin examinations every 6 months for the next few years.