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Today’s low mortgage rates might make your mouth water, but after shelling out hundreds of dollars for application fees and appraisals, a loan applicant may have the rug pulled out from under him.

Yes, the average 30-year fixed-rate loan is charging just 4.675%, according to the BankingMyWay survey. But getting the lowest rates advertized takes a virtually perfect credit history, and many borrowers who easily qualified in the past just can’t satisfy today’s jittery lenders.

Still, it may be worth it to get a loan even if you don’t get the lowest rate possible.

“Borrowers today are paying for the excesses of yesterday,” writes Jack M. Guttentag, emeritus finance professor at the Wharton School, on his website, The Mortgage Professor. “During the go-go years leading to the crisis, underwriting rules became incredibly lax, and now they have become excessively restrictive.”

Mortgage approvals are based on underwriting rules that stipulate things like how large the borrower’s income must be in relation to the loan, how clean the borrower’s credit history must be, and the percentage of the home’s purchase price that can be financed.

To get the lowest advertised rates, a borrower must have a credit score of 740 out of a possible 850, Guttentag says. Nearly 60% of people with credit scores fall below that 740 threshold.

To get the lowest loan rate, the borrower also must have a loan-to-value ratio, or LTV, of no more than 60%, Guttentag says. That means you’d need a $120,000 down payment to buy a $300,000 home.

This may explain why such a high percentage of new mortgages, about four out of five, are being refinanced. Many of these borrowers already have a lot of equity in their properties, enough to satisfy the demanding LTV requirement. Also, many would-be first-time home buyers simply don’t have enough cash, and are getting shut out.

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The big players in today’s mortgage market are Fannie Mae (Stock Quote: FNM) and Freddie Mac (Stock Quote: FRE). Both buy mortgages from lenders and bundle them into securities that are sold to investors. To protect the securities’ quality, the two firms set minimum underwriting standards.

If a loan does not pass, the original lender is required to buy it back, causing a loss to the lender who then wipes out the profit it would make on eight loans of a similar size, says Guttentag. Lenders, therefore, are being very conservative about approving loans.

The tougher standards have been especially hard on self-employed applicants because lenders fear their incomes are not secure.

“Rejection of loan applications by self-employed borrowers with high credit scores and ample equity are now commonplace,” Guttentag says.

Loan applicants who do not qualify for the lowest rates advertised shouldn’t give up, however. Even if you paid 6% or 7%, well above the heavily promoted rates that are below 5%, you’d still have a rate that’s pretty low by historical standards. Use the Maximum Mortgage Calculator to see how large a loan you might get at various interest rates.

Of course, you also can consider buying a cheaper property, making it easier to qualify with any given income. Or you could sell some other investments to produce a bigger down payment.

Finally, you can wait. If the economy improves, lenders are likely to ease their requirements a bit. After all, they want to lend, as long as they’re confident they’ll be paid back. Waiting to buy may mean passing up the dream home you spot today, but you’ll probably have plenty of other chances, as most experts expect home prices to stay low for several years at least.

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