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Ensembl Ref/alt allele discrepancy

Hello,

While exploring rs72552763 INDEL in Ensembl, the Alleles field show the ref and alt allele as ATGAT/AT. However, in the following line that provides location, the VCF shows ref and alt allele as ATGA A

Here's the screenshot for reference.

Why is there a discrepancy in ref/alt alleles? I am not sure if I am missing something obvious here. Any help to understand this discrepancy will be highly appreciated!

Thank you very much!

ensembl indel dbsnp vcf variant
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updated by Mwangana • Mwangana • written by patelk26 patelk26

2 answers

Hi patelk26 - this is just two different ways of representing the inframe deletion of 'TGA' according to either the Ensembl default or VCF specifications: https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#input

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written by Ben Moore Ben Moore

Thank you for your prompt response. This is a naive question. I get confused because when I look at dbSNP record, it indicates the bases GAT are deleted, unless I am interpreting the record incorrectly. Could you please help clarify this? Thanks again!

enter image description here

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written by patelk26 patelk26

It's both an ATG deletion and a GAT deletion. This is essential a variant normalization issue. However, when GAT is used, the coordinate should change. So I assume 2nd report you posted is wrong.

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written by Zhenyu Zhang Zhenyu Zhang

Thank you for your comment. I guess this add more to my confusion. Is it an TGA/GAT deletion like Ben_Ensembl suggested, or ATG deletion?

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written by patelk26 patelk26

As Zhenyu Zhang said, this is a variant normalisation issue. For example, you could remove 'ATG', 'TGA' or 'GAT' from 'ATGAT' and be left with 'AT'. Different variant notation formats have different ways of dealing with this ambiguity, for example, VCF describes variants using their most 5’ representation, while HGVS format describes a variant at its most 3’ location.

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written by Ben Moore Ben Moore

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