Tip:
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In this video I’ll show how to use the capability in the graphical view to search for positions using HGVS terminology.
I’ll start with my web browser open to the Gene page at NCBI.
Here, I’ll search for the gene FGFR3.
From the results page, I’ll select the first item.
Then I’ll scroll down to the graphical view.
In the find box, I’m going to type an HGVS expression. I’m going to type:
N M _ 0 0 0 1 4 2 . 4 :
c . 1 9 4 9 a > t
When the location is found, a locked marker appears.
The marker’s locked by default so you don’t move it accidentally.
From here, I’ll mouse over the marker and hover
When the menu appears, I’ll select ‘zoom to sequence at marker.’
I might have to zoom in a little further.
Here I can see the ‘A’ and if I hover over the SNP
I can see the allele A>T change.
If I go back and hover over the marker.
I can select ‘Marker Details’ and I see all the other annotation at this location
which includes converting this HGVS expressions for all others based on other RefSeqs.
I can also search for an rs number.
So if I pick this one, it’s rs104886006
If I type that in find box and press return
Again we see a locked marker that appears in this location.
Again if we hover over the marker, we can click on ‘Marker Details’
And see all the annotation at this location including the HGVS coordinates.
Because it’s the second marker, we have to scroll down to the bottom half.
As always, there’s more you can do with these tools. Please visit the NCBI website.