Transcripts and exon number in Integrative Genomics Viewer (IGV)

[vipul jain]

Hi..

I am doing variant analysis and I want to know the exon number of a variant using IGV. In IGV it shows different exon numbers for different transcript of a gene so which transcript should I consider.

It would be great if anyone help me in this regard.

[GenoMax]

Depending on the isoform the transcript number and the exon number may change but the genomic position of the SNP is constant. Keeping track of the transcript ID along with the exon number would be best practice (since according to NCBI Gene Record for ESR1):

Alternative promoter usage and alternative splicing result in dozens of transcript variants, but the full-length nature of many of these variants has not been determined.

[vipul jain]

Depending on the isoform the transcript number and the exon number may change but the genomic position of the SNP is constant. Keeping track of the transcript ID along with the exon number would be best practice (since according to NCBI Gene Record for ESR1):

Thanks. In case I have to select single exon & transcript then which one I should select

[GenoMax]

What is the reason you can select only one? Any isoform you choose is still ESR1.

[vipul jain]

What is the reason you can select only one? Any isoform you choose is still ESR1.

I need to give report to doctors in which I have to mention exon no. and codon position of a variant. there is no option of transcript id in report format.

[GenoMax]

Since the genomic coordinate of the SNP is invariant you should report that along with the gene name (making a note of the genome build, which is hg19 in your example). Unless you are doing full length transcript sequencing you can't say for sure which exact transcript the reads are coming from.

[vipul jain]

Thanks for the valuable information.