df[!duplicated(df[cdf[ , c("id","gender")]),]
# id gender variant
# 1 1 Female a
# 3 1 Male c
# 4 2 Female d
# 5 2 Male e
Another way of doing this using subset as below:
subset(df, !duplicated(subset(df, select=c(id, gender))))
# id gender variant
# 1 1 Female a
# 3 1 Male c
# 4 2 Female d
# 5 2 Male e