<$fh> will read a single line from your file, so just add two of them:

open (my $fh,”<”,$file) or die “Can’t open file $file: $!”; 

<$fh>; # discard first
<$fh>; # two lines

while (my $line = <$fh>) { 
    chomp($line); 

    #blah
}
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