Players are not allowed to assemble clubs on the course under rule 4.1b(4), which states that one cannot "build a club from parts carried by anyone for the player during the round".
Varner damaged his driver warming up before his round and sent a representative to retrieve a replacement and bring it to him on the course.
However, Varner wanted to use the shaft of the damaged club, so when the replacement arrived he attached the new head to the old shaft.
"They don't want clubs assembled and adjusted on the golf course, so that's the reason for that rule," PGA Tour rules official Mark Russell told reporters.
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"The rule basically says a player must not build a club from parts carried by anyone for the player during the round."
Varner shot two-over-par 74, including the penalty, which left the American nine strokes off the lead.
(Reporting by Andrew Both in Cary, North Carolina, editing by Ed Osmond)
