A couple of other ways to look at this.
Method #1
Since you only are interested in lines if they have more than 2 characters separated by commas you could just grep for commas:
$ grep "," sample.txt chr2 3323 C T,A chr3 5251 C T,G chr3 9990 G C,T Method #2
You could use grep's PCRE facility. This is where grep can use Perl's regular expression engine to do the matching. It's quite powerful and lets you do a lot of what you can do with Perl from grep.
loosely defined
$ grep -P "(\w,)+" sample.txt strictly defined
$ grep -P '\w+\d\s+\d+\s+\w\s+(\w,)+' sample.txt Method #3
Using awk. This again is taking advantage of the fact that only the lines with a comma (,) are of interest, so it just finds them and prints them:
loosely defined
$ awk '/,/{print}' sample.txt more strictly defined
$ awk '/([[:alpha:]])+,[[:alpha:]]/{print}' sample.txt even more strictly defined
$ awk '$4 ~ /([[:alpha:]])+,[[:alpha:]]/{print}' sample.txt This one looks at the contents of the 4th column and checks that it's a letter followed by a comma, followed by another letter.
even more strictly defined
$ awk '$4 ~ /([GATC])+,[GATC]/{print}' sample.txt This looks for only a G,A,T, or C followed by a comma, followed by another G,A,T or C.