How can I remove specific rules from iptables?

The best solution that works for me without any problems looks this way:
1. Add temporary rule with some comment:

comment=$(cat /proc/sys/kernel/random/uuid | sed 's/\-//g')
iptables -A ..... -m comment --comment "${comment}" -j REQUIRED_ACTION

2. When the rule added and you wish to remove it (or everything with this comment), do:

iptables-save | grep -v "${comment}" | iptables-restore

So, you'll 100% delete all rules that match the $comment and leave other lines untouched. This solution works for last 2 months with about 100 changes of rules per day - no issues.Hope, it helps

Execute the same commands but replace the "-A" with "-D". For example:

iptables -A ...

becomes

iptables -D ...

You may also use the rule's number (--line-numbers):

iptables -L INPUT --line-numbers

Example output :

Chain INPUT (policy ACCEPT) 
    num  target prot opt source destination
    1    ACCEPT     udp  --  anywhere  anywhere             udp dpt:domain 
    2    ACCEPT     tcp  --  anywhere  anywhere             tcp dpt:domain 
    3    ACCEPT     udp  --  anywhere  anywhere             udp dpt:bootps 
    4    ACCEPT     tcp  --  anywhere  anywhere             tcp dpt:bootps

So if you would like to delete second rule :

iptables -D INPUT 2

Update

If you use(d) a specific table (eg nat), you have to add it to the delete command (thx to @ThorSummoner for the comment)

sudo iptables -t nat -D PREROUTING 1

First list all iptables rules with this command:

iptables -S

it lists like:

-A XYZ -p tcp -m state --state NEW -m tcp --dport 22 -j ACCEPT

Then copy the desired line, and just replace -A with -D to delete that:

iptables -D XYZ -p ...