WASHINGTON - The refinancing boom has made a slight dent in Fannie Mae's net interest margins but has not noticeably slowed the growth of its earnings.

Its third-quarter report, released last weeks, showed earnings had climbed to $477.2 million from $412.9 million in the same quarter last year. Earnings in the second quarter this year were $458.8 million.

Interest income from loan held in portfolio, guarantee fees from mortgage-backed securities, and Remic fees all went up in the third quarter.

"Every item of revenue went up, and expenses went down. That shows considerable earnings power," said Paul Paquin, senior vice president at Fannie Mae.

Lawrence M. Small, Fannie's president, said the third-quarter performance was fueled by record business volumes. "We now expect total business volume for all of 1993 to be close to $300 billion."

High refinancing volume drained the portfolio of high-interest loans and caused the interest margin to shrink to 1.34% from 1.29% in the same quarter last year. The interest margin is the difference between the cost of funds and the yield on Fannie's portfolio loans.

Still, because Fannie's portfolio grew substantially, the company came out ahead. Its net interest income was $661.7 million compared with $506.9 million in the third quarter last year.

High refinance volume fuel portfolio growth because Fannie can buy loans at attractive prices from lenders, Mr. Paquin explained.

Fannie's net mortgage portfolio was $179 billion at the end of the third quarter, compared with $170 billion at the end of the second quarter and $143 billion at the end of the third quarter last year.

The company tooks steps again in the third quarter to buy back $5.6 billion in high-coupon debt, and refinance it at a lower cost that better matches the lower-yielding mortgages it is now buying.

Fannie Mae reported $79.7 million in pretax losses, related to the calling or repurchasing of debt. Fannie called or repurchased $3.6 billion in the second quarter of 1993 and $2.7 billion in the third quarter of 1992. It took pretax losses, respectively, of $60.3 million and $14.2 million.

Mr. Paquin said the company expects to call more premium debt in the fourth quarter and take pretax losses of roughly $31 million.

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