Zebrafish Genome Literacy Workshop 2023

Exercise 4 - exploring variation

The missense variant rs180018766 is found in the zebrafish ift88 gene. Find the page associated with this variant in Ensembl. How many transcripts does ift88 have and in how many of them is rs180018766 a missense variant?

5 transcripts. Missense in 3.

Does the rs180018766 have a consequence for any other genes? If so, what's the ZFIN symbol for that gene?

Yes, rs180018766 is an upstream variant of il17d.

What is the reference allele for rs180018766 and what is the alternative or variant allele?

T; C.

What is the HGVS name (Human Genome Variation Society nomenclature, which, despite the name, is useful for other organisms too) for this variant with respect to the ENSDART00000110943 transcript?

ENSDART00000110943.5:c.2326A>G.

Why does that HGVS name indicate the variant involves an A to G change, whereas the alleles are listed as T and C?

The gene is on the reverse strand. The reference and alternative alleles are shown in the context of the genome, whereas the HGVS name is in the context of the gene.

Does SIFT predict that the rs180018766 missense variant will be deleterious or tolerated?

Tolerated.

Follow the link to view the rs180018766 variant in EVA (the European Variation Archive). In how many sequencing projects has this variant been found?

3.

Find the variant table for ift88. It shows the known variants for the gene. How many other missense variants are known in ift88?

Just 1. Note that the table has 7 rows, but 3 are rs180018766 and 4 represent one other variant.

You have resequenced the atp5po gene (ENSDARG00000001788) and found three variants:

• C/T at 9:33146126
• A/G at 9:33147350
• A/C at 9:33148752

Use the Ensembl VEP tool to predict the consequences of these three variants. What are the consequences of the three variants on the canonical transcript of atp5po?

synonymous_variant, intron_variant and 3_prime_UTR_variant.

Using https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html to help you, which of these consequences is predicted to have a low impact on the protein?

synonymous_variant.

Have any of these three variants been found before?

Yes, the G variant at 9:33147350 is rs180140691.