...
while ( <$inFH> )
{
    my @tags = split;
    next unless $tags[ 1 ] eq q{NN};
    
    $hash{ $tags[ 2 ] }->{ frequency } ++;
    push @{ $hash{ $tags[ 2 ] }->{ variants } }, $tags[ 0 ]
       unless $hash{ $tags[ 2 ] }->{ seen }->{ $tags[ 0 ] } ++;
}

delete $hash{ $_ }->{ seen } for keys %hash;
...