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He was the son of William Spencer (1769–1834), younger son of Lord Charles Spencer, and a great-grandson of Charles Spencer, 3rd Duke of Marlborough; his German mother Susan being a Countess of the Holy Roman Empire.
Spencer was the son of Robert Spencer, 1st Baron Spencer of Wormleighton, and his wife, Margaret Willoughby, and was baptised on 4 January 1591 at Brington, Northamptonshire.