gnomad database doesn't agree with browser?

[Billy Cvammen]

Hello from Ohio!

We have noticed that our list of human gene variants in the HMGXB4 gene from the GNOMAD server differs from the map of the same gene in the genome browser. The nucleotide numbering for the human variants starts at 35,653,557 and ends at 35,689,636 (having been filtered for variants more likely to have phenotypic consequences), whereas the UCSC browser starts the gene at 35,265,000 and ends it at 35,295,000. Can you provide any guidance for how we can adjust for the discrepancy?

 

I am an undergraduate doing research with gene variants. Thank you for any help you can give me.

Billy Cvammen

 

Sent from Mail for Windows 10

 

[Robert Kuhn]

Hello, Billy,

I believe you may be looking at a different genome assembly.  At UCSC

we display the last five official assemblies.  The coordinates for genes

change with every assembly release.  The gene coordinates on hg38, 

the default assembly at ucsc, for your gene are:

hg38  chr22:35,257,498-35,295,764

The hg19 assembly has these coordinates:

hg19  chr22:35,653,445-35,691,800

Does this account for your differences?  The start point for the gene on hg38

does not match the coordinates you report, but much of the 5' end is non-coding

or intron and is maybe not included in your interval because you have

>  filtered for variants more likely to have phenotypic consequences

?

If this does not resolve your problem, please let us know and we will look into

it further.

thanks and best wishes,

    --b0b kuhn

    ucsc genome bioinformatics group

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