I know this isn't what you asked, but I'm not following the logic of the regexes. Are you trying to remove whitespace before and after the input? If so, make it part of what you split on:

my @vars = split(/\s*,\s*/,$rec);
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Also, if you are only interested in $var3 for the hash, why work on the rest? Do something like:

open (DATA, "<data.txt") or die "Can't open file $!\n";
  @DATA = <DATA>;
  close (DATA);

  foreach $rec (@DATA) {
      chomp $rec;
      my @vars = split(/\s*,\s*/,$rec);
      # debug - you might want to join with '|' to see
      # whitespace in any vars
      print "VARS = " . join('|', @vars). "\n";
      # now insert into the hash
      $var_hash{$vars[2]} = 'whatever';
  }
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If you could relay more info the format of the input and how you want to make use of the hash you might get more (better) suggestions.

best of luck

--telesto