Here is the final ugly code.

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

my %info = (); 
my ($gi, $humangi, $accession);

my $data = '/DATA/proteinfile.txt'; 
open INFILE, '<', $data or die "Failed at opening $data!\n";

# Construct the hash with GIs as keys and sequences as values
while ( <INFILE> ) {
my $line = $_;
chomp($line);
    last if m!END!;
	
	if($line=~m/HUMAN/){
		
		($humangi) = ($line=~m/^\S+\|(\d+)/);
		
	   ($accession) = ($line=~m/^\S+\|\d+\|\w+\|(\S{6}?)/);
	   
	  	}
	
	if($line=~m/^\S+\|(\d+)/)
	   {
	    if(defined($1))
		 { 
		  $gi=$1;
		 }	
	   }
	else
	   {
	    $info{$gi} = $line;
		}
}
	#print Dumper (\%info);

	print "$humangi\n";
	print "$accession\n";

close(INFILE);

my $data2 = '/DATA/variantlist.txt'; 
open INFILE2, '<', $data2 or die "Failed at opening $data2!\n";

my $data3 = '/DATA/VariantOutput.txt'; 
open OUTFILE, '>', $data3 or die "Failed at opening $data3!\n";

print OUTFILE "This is [GI: $humangi] and [Accession: $accession]\nVARIANT\t\tPOTENTIAL\t\tPD\n";

while ( <INFILE2>){
# Grab a variant from the file (in this example: P82L)
my $line2 = $_;
chomp($line2);
my $Variant = $line2;

# Split the variant into three parts
my ($source, $position, $sink) = split(/(\d+)(\w)/, $Variant);

#print "$source\t$position\t$sink\n";
# Check whether HS has the source (i.e., P) at the given position (i.e., 82)
my $temp = $info{$humangi};

	#print "Temp contains $temp" . "\n";
	
my @char = split //, $temp;	

	#print "Now \@char contains: @char";

	#print "Inside the temp: $char[0] and $char[1]\n";

my $target = $char[$position-1];
	
	#print "This is the target: $target" . "\n";

if ( $target eq $source) {
	
	 print "Yep!\n";
	}
	
my @VariantList = ();
my @PDList = ();
	
# Scan the rest of the sequences to check what amino acid they have at the given position
for my $gi ( keys %info ) {
        my $value = $info{$gi};
		
		my @char2 = split //, $value;
		
		my $potential = $char2[$position-1];
		
		push (@VariantList, $potential); 
		
		
		if ($potential eq $sink){ # Note the cases where we observe the sink (i.e., L) at this position
			
			my $pd = "$potential" . "{" . "$gi" . "}";
			
			push (@PDList, $pd) 			
			#print "A pathogenic deviation has been found at site $position - from $source to $sink !\n" . " And the corresponding gi for this deviation is: $gi\n";
			
			}
			}

print OUTFILE "$Variant\t\t@VariantList\t\t@PDList\n";
}
close(INFILE2);