Question

Sanger validated SNP not present in IGV despite 10X coverage at site??!!

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6.8 years ago

rb14sp ▴ 40

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

NGS IGV Sanger • 2.2k views

ADD COMMENT • link updated 6.8 years ago by finswimmer 16k • written 6.8 years ago by rb14sp ▴ 40

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Can you exclude the possibility of a sample swap?

ADD REPLY • link 6.8 years ago by WouterDeCoster 47k

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No sample swap, we've confirmed

ADD REPLY • link 6.8 years ago by rb14sp ▴ 40

score 2 · Answer 1 · 2018-03-14

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

score 0 · Answer 2 · 2018-03-13

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).