UCSC variant annotation integrator error: gpFxCheckTranscript: expecting insertion

Question

[timodonnell]

I'm hitting frequent errors using the UCSC variant annotation integrator. I'm new to variant annotation, so I'm wondering if someone can spot an obvious mistake I'm making here. Here is the error I'm getting:

gpFxCheckTranscript: expecting insertion in pred=uc031qqx.1 but varStart=107281145, varEnd=107281145, vieStart=6, vieEnd=4, starts in exon, ends in exon

This is presumably related to this line in my VCF:

chr14   107281145   .   A   AC  373.73  .   AC=2;AF=1.00;AN=2;DP=12;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.15;MQ0=0;QD=31.14 GT:AD:DP:GQ:PL  1/1:0,12:12:36:411,36,0

If I delete the problematic line, the analysis continues, but then hits a similar issue later. Any thoughts on what's going on?

Thanks!