As mentioned in MyGene.info's year-end review, the team behind both services have been very productive. In addition to all the work they did on MyGene.info (and the back-end/BioThings services behind both MyGene.info and MyVariant.info, they made the following improvements to MyVariant.info this year:
-2016.01.06: ClinVar data structure overhauled

-2016.01.18: ClinVar data updated
-2016.07.18: Support for GRCh38/hg38 added

-2016.08.22: Python client updated to v0.3.1
-2016.08.25: Additional ExAC data added/updated

-2016.09: Starting this month, ClinVar data is updated on MyVariant.info on a regular basis.
-2016.10.03: https enabled

-2016.11.30: API status added to site

Also as mentioned in the year-end post for MyGene.info, there were two particular resources that we very excited about:

First, CIViC, which had been using MyGene.info, but recently incorporated MyVariant.info

Second, MyGene2, which is one of six finalists for the Open Science Prize and will potentially impact researcher work and rare disease patient lives alike. Note- Voting for the Open Science Prize is open until January 6th, so you can still vote for MyGene2.

Before we get to the best thing about 2016 for MyVariant.info, here's what the MyVariant team has been up to in terms of spreading the word about this service.
-2016.01.22: Chunlei gave an update for Heart BD2K technical conference call

-2016.03.29: The paper for Mygene.info/MyVariant.info was accepted to Genome Biology
-2016.04.05: Kevin presented at ISCB's NGS 2016 conference

-2016.05.10: Corresponding press releases were published to Eureka Alert and Science Daily
-2016.05.25: MyGene and MyVariant were featured in a post on the Genome Biology blog
-2016.05.30: Chunlei was interviewed for Rarecast podcast about the services

-2016.06.09: The MyGene/MyVariant services were invited for a guest post on the Elasticsearch blog
-2016.07.10: Kevin did a poster presentation at ISMB 2016

-2016.07.12: Chunlei also presented at ISMB 2016
-2016.11.29: Chunlei presented at BD2K AHM 2016

-2016.11.28-30: Kevin presented a poster at the same meeting

Finally...MyVariant.info broke the record on usage. In just two years, MyVariant.info went from having just a fraction of the usage that MyGene.info had, to having about double MyGene's traffic. For 2016 (as of December 22nd), MyVariant.info had almost 116 Million sessions according to google analytics.