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, but listing it as being intergenic near that gene. gnomAD itself 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?