$gen_seq_list{'42-MG-BA'} = (
      '19_35770059' => 'TC',
      '2_68019584'  => 'G',
      '16_9561557'  => 'G'
   );

##</code><code>##

   for my $seq (keys %$gen_seq_list) {
      for (keys %{$seq}) {
         if ($gen_seq_list{$seq}{$_} == $cave_snp_list{$seq}{$_}) {
            ...
         }
      }
   }

##</code><code>##

use strict;
use warnings;

my %genes = (
   '42-MG-BA' => {
                    '19_35770059' => { cave => 'TC', gen => 'AA' },
                    '2_68019584'  => { cave => 'G' },
                    '16_9561557'  => { gen  => 'AG' },
                 },
   '41-OK-DZ' => {
                    '7_158773210' => { gen => 'AA', cave => 'G'},
                 },
);

for my $gene (keys %genes) {
   for my $seq (keys %{$genes{$gene}}) {
      my $href = \%{$genes{$gene}{$seq}};
      if (keys %$href > 1) {
         print  "$gene:$seq:",
                join(",", map {"$_=$$href{$_}"} keys %$href),
                "\n";
      }
   }
}
__OUTPUT__
41-OK-DZ:7_158773210:gen=AA,cave=G
42-MG-BA:19_35770059:gen=AA,cave=TC