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As you can see, that variant is localized in 4 transcripts. The annotation is a missense variant for 3 transcripts of that gene and the fourth transcript is a noncoding transcript (i.e. it has no known protein product). As such the annotation is for the fourth that this variant is localized in an exon of a non coding transcript. You can see this gene in Ensembl: http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000198959;r=20:38128461-38133760;t=ENST00000469269 And indeed, there are both coding and non-coding transcripts.

"Wild-type" isn't the correct term in (human) population genetics. I'd say every one of us is equally wild regardless of presence or absence of rare variants. The correct term and way of viewing this would be "reference allele", meaning the allele which was found when constructing the human reference genome (using a few donors - not one sample). Therefore, it's very well possible (and indeed happens as you see) that the reference allele isn't the major allele.