The FHA loan limit for the county where I am buying home is 729,750 for a single family. I am buying a home for 500,000 and financing 475,000 with 5% down. My mortgage broker is quoting me 5.375% for the loan even though the best FHA rate on the mortgage company website is 5%. When I ask him he said my loan is still considered high balance and hence the extra 0.375% on the rate quoted  to me. I am unable to understand this, the loan limit is 729,750 for my county, why should 475,000 be considered high balance

FHA loans have a two categories right now, a "standard" FHA if you will, up to a loan amount of $417K and Jumbo FHA, anything above that up to the limit of $729,750.  There is different pricing for these temorary Jumbo FHA's of anywhere from .25% to .5% higher depending on the lender.  That said, 5.375% could be a bit on the high side but, as always, it's never just the rate.  It depends on the points being paid if any, when the rate was locked (if it's locked), the term of the lock, among other things.