Question: Sanger validated SNP not present in IGV despite 10X coverage at site??!!
1
gravatar for rb14sp
3 months ago by
rb14sp40
rb14sp40 wrote:

Hi,

Sanger validation has shown that there is a c.26T>C variant detected in REEP1. The genomic coordinate is chr2:86564608. There is a read depth of ~10 at this position but no variant. Will someone offer their thoughts about this and why it was not picked up by exome sequencing?

Thanks - Robert

Screen Shot 2018 01 30 at 1 35 41 PM

igv ngs sanger • 225 views
ADD COMMENTlink modified 3 months ago by finswimmer2.8k • written 3 months ago by rb14sp40
1

Can you exclude the possibility of a sample swap?

ADD REPLYlink written 3 months ago by WouterDeCoster29k

No sample swap, we've confirmed

ADD REPLYlink written 3 months ago by rb14sp40
2
gravatar for finswimmer
3 months ago by
finswimmer2.8k
Germany
finswimmer2.8k wrote:

Hello,

you are looking on the wrong position. In hg19 chr2:86564608 has a T. "c.26T>C" is the HGVS nomenclatur. As REEP1 encodes on the reverse strand you are looking for an A on your reference.

REEP1 has several transcripts with different coding exons. I guess the one you are showing is NM_001164730 (ENST00000538924.1). I think the correct transcript for you is NM_001164731 (ENST00000535845.1). Because here you can have a "c.26T>C". In hg19 the chromosomal position is chr2:86491163.

fin swimmer

ADD COMMENTlink modified 3 months ago • written 3 months ago by finswimmer2.8k
0
gravatar for Devon Ryan
3 months ago by
Devon Ryan80k
Freiburg, Germany
Devon Ryan80k wrote:

Perhaps the bait for that region happens to be designed in a way such that that variant is pulled down with low affinity. Alternatively, the sanger results could be wrong (not that I'd hold my breath) or you just got unlucky (presuming this was a heterozygous variant, so you just randomly got all 10 reads from the other allele).

ADD COMMENTlink written 3 months ago by Devon Ryan80k
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