Why is HGVS notation not available for some variants?
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3.4 years ago
jpuntomarcos ▴ 40

I have observed that VEP online (GRCH37) does not produce HGVS notation for some variants. For example giving this input:

1   45796269    45796269    G/C -

VEP produces results where HGVSc field is empty for all of them. However, this HGVS notation is produced for other variants. Any idea of why is this notation not being produced sometimes?

ensembl vep HGVS • 832 views
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3.4 years ago
Titus ▴ 910

I think it' because your variant is the intron part, introns are not composing the cDNA.

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This is correct (official Ensembl response)

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It's an intronic variant... However, VEP produces HGVS notation for this intronic variant:

4   55161254    55161254    C/T +

We can compare results for this variant and results for the first intronic variant in the post.

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