A few things...when you reference a column in a dataframe by name, you can'tuse quotation marks. Furthermore, when using dplyr functions, it assumes that you are using the dataframe you passed into the functions, so there's no need for the df$ before a column name. To filter the AF column in this dataset (unclear if dataset is called maf or maf.db so I'll assume the former) to include values <=0.01 and the blank spaces, try

maf.2 <- filter(maf,AF <= 0.01 | AF == "")

Which is equivalent to

maf.2 <- maf |> filter(AF <= 0.01 | AF == "")

if you want to practice using the pipe also!