How to find genomic coordinates of specific deletion in the HR gene?

Question

[abc.faisal]

We have found a novel deletion (429delC) in exon 2 of HR gene. I would like to find genomic coordinates of this location (may be based on GRCh37 assembly). Is there any easy solution for it?

[Santosh Anand]

And what are your reference exons?

[abc.faisal]

. The HR gene was amplified by specially designed oligonucleotide primers and the PCR products were purified by shrimp alkaline phosphatase and exonuclease enzymes and sequenced by using 3130 Genetic Analyzer (Applied Biosystems, Foster City, CA). I think it is RefSeqGene

[Santosh Anand]

Again, which RefSeq gene / sequence it refers to?

Do you have sequences of flanking regions? The do a BLAT https://genome.ucsc.edu/FAQ/FAQblat

[GenoMax]

OP is referring to HR gene.

[Santosh Anand]

A Gene can have multiple isoforms or transcripts. Moreover, the annotation of transcripts from different places can differ. So, one needs the reference sequence or transcript name to know exactly which transcript, as the coordinate is relative to that only.

[finswimmer]

You are absolutely right. To get an unambiguous result for sure, one needs the transcript, transcript version and reference genome.

But Ensembl's VEP accept also inputs, that might produce ambiguous results. It's the responsibility of the user to read these results correct.

fin swimmer

[Santosh Anand]

But Ensembl's VEP accept also inputs, that might produce ambiguous results

Good to know, thanks and +1 :) I did not expect this to be a known annotated variant!

[Santosh Anand]

And if you don't have the flanking regions, get the sequence of 2nd Exon from UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables) and count the location manually

[cpad0112]

try: This annotation is for GRCh 37. At the end (hgvsg section), you will find all possible genomic coordinates. caution from ensembl:HR:c.429delC may resolve to multiple genomic locations"

https://grch37.rest.ensembl.org/variant_recoder/human/HR:c.429delC?content-type=application/json

Answer 1

[finswimmer]

• Ensembl's VEP

[abc.faisal]

How? I do not have any genomic coordinate?

[finswimmer]

You just need to paste your gene and variant description into the data field. In your case the input looks like this: HR:c.429delC

That's all. The result includes the genomic region.

fin swimmer

[GenoMax]

If it is the HR gene I posted a link for above you do have that info.

NCBI version or Ensembl (which you would use with VEP).