Prediction of novel variants

Question

[syedahamdani94]

Hi everyone,

What does "." dot represents in dbSNP column of Annovar output, does it verifies novel variants? How can we identify novel variants from annovar output. Your suggestion will be really appreciated.

Thanks

[ATpoint]

It means the variant is not in the dbSNP release that the annotation tool used. That does not imply that the variant is true (means not a false-positive), nor that it is novel, somatic, biologically-meaningful, valuable or anything else. It just means that it is not in this given database. Can well be that 20 papers already described that variant without submitting it to dbSNP.

[syedahamdani94]

Thanks for your help @ATpoint. Appreciated!

[Hamid Ghaedi]

Just to add to the @ATpoint comment: The "." is a default option for Annovar to indicate "no result finding in the databases" . Not only in the dbSNP column, also in other columns you may find this "."!!

To get to know whether or not a variant is a novel, you may want to check the GnomeAD database also.

[syedahamdani94]

Thanks for suggesting GnomeAD, It saved my time. Grateful!