You could add another level below variants

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my %hash;
while (my $line = <DATA>){
  my ($tag1, $tag2, $tag3) = split /\t/, $line;
  if ($tag2 =~/NN/) {
    ++$hash{$tag3}{frequency};
    ++$hash{$tag3}{variants}{$tag1};
  } 
}

print Dumper \%hash;
[download]