# Mismatched variant consequences between OT Genetics VEP data and the OT Platform evidence page?
**URL:** https://community.opentargets.org/t/mismatched-variant-consequences-between-ot-genetics-vep-data-and-the-ot-platform-evidence-page/656
**Category:** Data issue
**Tags:** genetics-portal
**Created:** [8 June 2022 13:38 UTC](https://community.opentargets.org/t/mismatched-variant-consequences-between-ot-genetics-vep-data-and-the-ot-platform-evidence-page/656 "2022-06-08T13:38:14Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@fedde](https://community.opentargets.org/u/fedde)
#### Post date: [8 June 2022 13:38 UTC](https://community.opentargets.org/t/mismatched-variant-consequences-between-ot-genetics-vep-data-and-the-ot-platform-evidence-page/656/1 "2022-06-08T13:38:14Z")
The **VEP (Ensembl)** tab on `https://genetics.opentargets.org/variant/1_169681903_G_A` lists that, in the gene C1orf112 (ENSG00000000460), that variant’s most severe consequence is that it is _intronic_. The **GWAS lead variants** table on the same page shows that the variant came up in (among others) a study titled “Acne (severe) [fixed effect model]”. This association does appear [in the platform](https://platform.opentargets.org/evidence/ENSG00000000460/EFO_0003894), but listing it as being _intergenic_ near that gene. [gnomAD itself](https://gnomad.broadinstitute.org/variant/1-169681903-G-A?dataset=gnomad_r3) agrees with OT Genetics.
The discrepancy suggests to me that the ‘variant annotation’ (referenced on `https://github.com/opentargets/evidence_datasource_parsers#processing-genetics-portal-evidence`) used to generate `https://ftp.ebi.ac.uk/pub/databases/opentargets/platform/22.04/input/evidence-files/genetics-portal-evidences-2022-04-12.json.gz` was less complete/up-to-date than `https://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/22.02.01/v2g/`; the input files I linked currently match what their respective applications say.
This is only one example of many similar cases. Am I correct to be surprised by this difference or mistaken about how to read the data model?
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### Author:  [@dsuveges](https://community.opentargets.org/u/dsuveges)
#### Post date: [9 June 2022 09:31 UTC](https://community.opentargets.org/t/mismatched-variant-consequences-between-ot-genetics-vep-data-and-the-ot-platform-evidence-page/656/2 "2022-06-09T09:31:39Z")
Hi @fedde , you are right, this information should be consistent across the Genetics Portal and the Platform. We are taking a look at the logic how the Platform evidence is generated.
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### Author:  [@ochoa](https://community.opentargets.org/u/ochoa)
#### Post date: [9 June 2022 09:41 UTC](https://community.opentargets.org/t/mismatched-variant-consequences-between-ot-genetics-vep-data-and-the-ot-platform-evidence-page/656/3 "2022-06-09T09:41:40Z")
Issue opened
>
>
> As reported by @fedde-s in \[Community\](https://community.opentargets.org/t/misma…tched-variant-consequences-between-ot-genetics-vep-data-and-the-ot-platform-evidence-page/656)
>
> \> The VEP (Ensembl) tab on https://genetics.opentargets.org/variant/1\_169681903\_G\_A lists that, in the gene C1orf112 (ENSG00000000460), that variant’s most severe consequence is that it is intronic. The GWAS lead variants table on the same page shows that the variant came up in (among others) a study titled “Acne (severe) \[fixed effect model\]”. This association does appear \[in the platform 1\](https://platform.opentargets.org/evidence/ENSG00000000460/EFO\_0003894), but listing it as being intergenic near that gene. \[gnomAD itself\](https://gnomad.broadinstitute.org/variant/1-169681903-G-A?dataset=gnomad\_r3) agrees with OT Genetics.
> \>
> \> The discrepancy suggests to me that the ‘variant annotation’ (referenced on https://github.com/opentargets/evidence\_datasource\_parsers#processing-genetics-portal-evidence) used to generate https://ftp.ebi.ac.uk/pub/databases/opentargets/platform/22.04/input/evidence-files/genetics-portal-evidences-2022-04-12.json.gz was less complete/up-to-date than https://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/22.02.01/v2g/; the input files I linked currently match what their respective applications say.
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### Author:  [@dsuveges](https://community.opentargets.org/u/dsuveges)
#### Post date: [9 June 2022 20:48 UTC](https://community.opentargets.org/t/mismatched-variant-consequences-between-ot-genetics-vep-data-and-the-ot-platform-evidence-page/656/4 "2022-06-09T20:48:05Z")
Hi @fedde , We have identified the source of this discrepancy: for the Platform disease/target evidence we were picking the consequence on the canonical transcript of the gene. While other Genetics Portal (as well as GnomAD) uses the most severe consequence term across all transcripts.
In your example, the canonical transcript of this gene is the third from top.
Thanks for raising this issue. We are discussing how to go about this. We certainly make the two products consistent.