predictCoding VariantAnnotation TP53 bug

[IonTom]

I am trying to annotate some SNPs using the predictCoding function from the VariantAnnotation Bioconductor package. But for some reason it does not annotate some of my SNPs, for the other ones it works just fine.

The ones causing trouble are located in TP53.
like

chr17 [7578263, 7578263] + G A

This is clearly located in TP3 but for some reason predictCoding ignores it.

My code looks like this:

library(BSgenome.Hsapiens.UCSC.hg19)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

predictCoding(query=x,subject =txdb,seqSource=BSgenome.Hsapiens.UCSC.hg19,DNAStringSet(alt(x)))

where x is the GRanges/VRanges object containg the SNP in question.

I also tried generating my own txdb with
txdb <-makeTranscriptDbFromUCSC(genome="hg19", tablename="knownGene")

or

txdb <-makeTranscriptDbFromUCSC(genome="hg19", tablename="refGene")

both will not annotate it

i only get:

GRanges with 0 ranges and 1 metadata column:
GRanges with 0 ranges and 1 metadata column:
seqnames ranges strand | GENEID
<Rle> <IRanges> <Rle> | <character>
---
seqlengths:

Fot other SNPs it works fine