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Why has my fund balance increased but shares are missing from holdings?

Your shares can stop showing up in your holdings after you buy them if they are short delivered by the exchange. In such a scenario, you can either get the shares on the T+3 day or receive a credit in your funds balance.

When you buy a share, the person who has sold the shares is expected to deliver the shares to the exchange. If the person fails to deliver the shares, the trade is said to be short delivered.

The exchange conducts an auction to buy the short delivered shares. These shares are then delivered to you on the T+3 day. Sometimes, the exchange is not able to buy the shares on your behalf and settles the transaction in cash. TIn such a case, the exchange settles it in cash on the basis of the close-out rate. The close-out rate is the higher of the highest price of the stock from when you sell to the auction day or 20% above the closing price, on the auction day (T+2).

Check out this article to learn more about the close-out process.