Just add 1 ! before your pattern like this
sed '1 ! s/\(\([^,]*,\)\{9\}[^,]*\),/\1/g'
this would skip the header
Output
$ sed '1 ! s/\(\([^,]*,\)\{9\}[^,]*\),/\1/g' d
Name,Age,Gender,id,Phone,Address,City,State,Country,IPAddress,OtherColumn1,OtherColumn2
John,25,Male,12,123,Main St,New York,NY,USA,120.30.19 119.234.761,Value1,Value2
