Exploring variants of the zebrafish gene tbx16
(a) Find all of the splice region variants of the zebrafish tbx16 gene. How many splice region variants are annotated?
(b) What is the reference and variant alleles reported for the splice region variant rs180149499?
(c) Why does Ensembl put the A allele first?
(d) Where is the SNP located (chromosome and coordinates)?
(e) What is the HGVS recommendation nomenclature for this SNP?
(a) Go to www.ensembl.org. Type tbx16 in the Search box for zebrafish, then click Go. Select variant table from the side menu of the tbx16 gene page.
Select splice region variant from the consequence type filter.
(b) Select rs180149499.
The reported alleles are A/C/T. A is the reference allele. C and T are both reported variants.
(c) In Ensembl, the allele that is present in the reference genome assembly is always put first (A is the allele for the reference zebrafish genome).
(d) The variant is located on Chromosome 8, coordinates 51739646.
(e) Click on HGVS names to reveal information about HGVS nomenclature.
This SNP has got four HGVS names (two for each variant allele),
Variant allele T: NC_007119.7:g.51739646A>T ENSDART00000007090.9:c.953+6T>A
Variant allele C: NC_007119.7:g.51739646A>C ENSDART00000007090.9:c.953+6T>G