Why some annotations shown in TI do not match with Varsome?

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We show the Refseq canonical transcript annotations from Varsome in our applications. When a user clicks the info icon next to the variant in TI or Mosaic they are redirected to Varsome where they see more details for the variant and the details shown should match to that seen in the apps. This is not the case for some genes like TP53 and the reason is the use of MANE Select transcript by Varsome to display the annotations.

The Matched Annotation from the NCBI and EMBL-EBI (MANE) is a collaborative project that aims to converge human gene and transcript annotations and to define a genome wide set of representative transcripts and corresponding proteins for human protein-coding genes. Each MANE transcript represents an exact match in exonic regions between a Refseq transcript and its counterpart in the Ensembl/GENCODE annotation such that the two identifiers can be used synonymously.

As we still display the annotations for canonical transcripts defined by Refseq and not the MANE Select transcripts, there might be a difference in annotations seen in the apps vs Varsome. But if you scroll down to the Transcripts section of the Varsome page you can see that the Refseq canonical transcript details match to what is seen in our apps.

For example for TP53, NM_001276760.2 is used as canonical transcript by Refseq but NM_000546.6 is the MANE Select transcript for which the details are shown on the Varsome page. So the variant at position chr17-7577120-C-T seen as TP53:p.R234H in our apps is TP53:R273H by default in Varsome. Similarly TP53:R210T is TP53:R249T and TP53:R136H is TP53:R175H.


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