Shell Programming and Scripting

   if ($ClinSig !~/untested|unknown|not provided|other/i && $ClinSig ne "." && $ClinSig ne "|") {      
        $classification = $ClinSig;  
  } 
  elsif ($ClinSig !~/Pathogenic|Likely pathogenic|Uncertain significance/i || $ClinSig eq ".") {
             $classification = 'Likely Benign';
       }  
   else {
           if ($ClinSig=~/Pathogenic|Likely pathogenic/i" && $ClinSig ne ".") {
                 $classification = 'Pathogenic';
           }
        } 
elsif ($ClinSig=~/Uncertain significance/i && $ClinSig ne ".") 
                $classification = 'VUS';
     }

Only allow single keyword entries, like Pathogenic, that don't contain any of the regex, is not a ., and doesn't contain a |,a pipe character denotes multiple entries, like Benign|Likely benign.
In this case the default value of VUS remains and the conditions in the else statements will be used.

If $Clinsig contains any other words except what in the regex, or a .$classification is Likely Benign

If $Clinsig  contains any of the words in the regex and ., $classification is Pathogenic

If $Clinsig contains the words in the regex and  ., $classification is VUS

if ($ClinSig !~ /something/) {
   # This is not something
}
else {
    # Can ONLY be something
}

if ($ClinSig !~/untested|unknown|not provided|other|[.|]/i) {
   # Anything that it is not untested or unknown or not provide or other or dot or pipe
}
else {
   # Here can only be untested or unknown or not provided or other or dot or pipe.
   # It will never be Pathogenic or any other term except above. Even if you place it inside an if
}

if( $ClinSig =~ /something/ ) {
    # assignment for something
}
elsif( $ClinSig =~ /somethingElse/ ){
    # assignment for somethingElse
}
elsif($ClinSig =~ /notquiteSomething/ ){
    # assignment for notquiteSomething
}
elsif( $ClinSig =~ /likeSomething/ ) {
   # assignment for likeSomething
}

Argument "." isn't numeric in numeric gt (>) at /home/cmccabe/Desktop/NGS/scripts/classifier.pl line 35, <> line 16665.

line 16665
chrX	57313357	57313357	T	C	exonic	FAAH2	.	.	synonymous SNV	FAAH2:NM_174912.3:exon1:c.99T>C:p.G33G	rs2516023	0.9	0.53	0.73	0.35	0.29	0.22	0.29	0.41	0.9	0.51	0.37	0.22	0.3	0.38	0.42	0.49	0.88	0.27	0.5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	GOOD	82	hom	24	Likely Benign	.	.