I agree with you, it is very unusual to have this very low level BCR-ABL at diagnosis, with this amount of disease. I am assuming the karyotype did demonstrate the Philadelphia chromosome. I can think of two possibilities:
1-A lab error, and would suggest repeating the test
2-BCR-ABL variant, and would suggest a qualitative test for p190, p230, and other rare variants (maybe done at Mayo clinic)
Thanks,
Ehab Atallah (Wisconsin, USA)