With the publication of a new paper in Nature, the Exome Aggregation Consortium (ExAC) has received some much deserved attention on their open data/open access practice. ExAC variant annotation data has been available for awhile through MyVariant.info; however, their functional gene constraint data doesn’t fit well into MyVariant.info model. Speaking of ExAC annotations in MyVariant.info, check out the latest ExAC changes in this MyVariant.info post.

ExAC also released a computed “functional gene constraint” metrics for each transcript containing variants from ExAC dataset. Since this is at transcript/gene level, we have now imported this data into MyGene.info, instead of MyVariant.info (which is designed as variant-specific). You can now access ExAC’s latest release of functional gene constraint data from our v3 API of MyGene.info (under the field of exac). You can find out the definitions of all sub-fields under exac, or learn more about the functional gene constraint data from their FAQ and README files.

Ready to try pulling this new data? Try the following query examples:

If you use our python client, you’ll be pleased to know that the most recent update of our client also enables you to run similar queries.

Python example:

In [1]: import mygene

In [2]: mg = mygene.MyGeneinfo()

In [3]: mg.getgene(1017, fields='exac')  
In [4]: mg.getgene('ENSG00000153230', fields='exac')  
In [5]: mg.query('exac.transcript:ENST00000266970', fields='exac')  

Just want to mention again this new exac field is only available from our v3 MyGene.info API, not available from the still-live v2 API. Just another reason to switch to v3 API now :-).