Hello Sadaf,
I made a quick test on my side and it seems to be working fine:
I have defined different prices for my 2 variants:

Then I ran Sync Prices to Shopify.
Shopify has been updated with the correct prices per variant:

Can you please recheck your Sales Price on BC side?
Please check also if you have any Customer Price Group defined in your Shop and if the Sales Price is correctly setup for that Customer Price Group.
Hope this can help.