Flannery missed Ireland's summer and autumn international in 2010 as well as their 2011 RBS 6 Nations campaign through injury and although he was picked in Ireland's World Cup squad, a calf tear has now ruled him out of the rest of the tournament.
Ulster's Rory Best, who played at hooker against the USA in Ireland's World Cup opener, will continue against Australia on Saturday while Varley, who has two international caps to his name, hopes to arrive in Auckland in time to see the Wallabies clash.
And Varley, who started in Munster's RaboDirect Pro12 victory over Glasgow on Friday, admitted his joy at getting the nod but spared a thought for his injured teammate.
"There were a couple of emotions running through my head when I got the call inviting me to join up with the squad," said Varley.
"The first was obviously overriding elation at getting the opportunity to take part in the tournament.
"You always dream of representing your country at the highest possible level and the World Cup is the pinnacle of the sport.
"After the initial excitement, my thoughts turned to Jerry's position.
"I know he'll be gutted at having to return home early after what has been a hard journey for him to get his fitness back, but I am sure he will be looking to get back playing as soon as possible.
"The best possible compliment I can pay him is to make sure that I train hard down there and do whatever I can to help the squad be as successful as possible."
Varley failed to make the cut for Ireland's 30-strong travelling party but was part of Declan Kidney's 43-man provisional squad and as a result, he believes he will fit seamlessly into the set-up.
"I've been able to maintain my fitness levels with Munster and kept my game time ticking over with them, so I feel fresh and ready to do whatever is asked of me," he added.
"I was part of the extended squad for the pre-season, so a lot of the technical stuff and calls are still fresh enough for me to be able to hit the ground running."
63x46.png){kind=logo}