Variant Page Implementation - data and FE first scoping iterations summary ticket

[prashantuniyal02]

The team is currently iterating on MVP for datasets and design for a Variant Page, which would be a new addition to the Open Targets (new entity). This task is part of the discussion on how we can build a UI/web application from Gentropy.

We are now working on a page blueprint [link here], which contains dataponts and MVP design for the new page.

This ticket will capture all the above iterations, focusing on data and front-end (with BE iterations to be scoped in between).

[buniello]

• [ ] metadata section

To unblock FE work on the metadata section of the page, the data team have shared a metadata json:

{"variantId":"X_27135701_T_C","chromosome":"X","position":27135701,"chromosomeB37":"X","positionB37":27153818,"referenceAllele":"T","alternateAllele":"C","rsIds":["rs899125696"],"alleleType":"snv","alleleFrequencies":[{"populationName":"afr_adj","alleleFrequency":6.494560805325539E-5},{"populationName":"ami_adj","alleleFrequency":0.0},{"populationName":"amr_adj","alleleFrequency":0.0},{"populationName":"asj_adj","alleleFrequency":0.0},{"populationName":"eas_adj","alleleFrequency":0.0},{"populationName":"fin_adj","alleleFrequency":0.0},{"populationName":"mid_adj","alleleFrequency":0.0},{"populationName":"nfe_adj","alleleFrequency":0.0},{"populationName":"remaining_adj","alleleFrequency":0.0},{"populationName":"sas_adj","alleleFrequency":0.0}],"vep":{"mostSevereConsequence":"intron_variant","transcriptConsequences":[]},"inSilicoPredictors":{"cadd":{"phred":0.585,"raw":-0.172629},"pangolinLargestDs":0.01,"phylop":-0.246}}
{"variantId":"X_27135703_G_A","chromosome":"X","position":27135703,"chromosomeB37":"X","positionB37":27153820,"referenceAllele":"G","alternateAllele":"A","rsIds":["rs12557104"],"alleleType":"snv","alleleFrequencies":[{"populationName":"afr_adj","alleleFrequency":0.0},{"populationName":"ami_adj","alleleFrequency":0.0},{"populationName":"amr_adj","alleleFrequency":0.0},{"populationName":"asj_adj","alleleFrequency":0.0},{"populationName":"eas_adj","alleleFrequency":2.838489923360772E-4},{"populationName":"fin_adj","alleleFrequency":0.0},{"populationName":"mid_adj","alleleFrequency":0.0},{"populationName":"nfe_adj","alleleFrequency":0.0},{"populationName":"remaining_adj","alleleFrequency":0.0},{"populationName":"sas_adj","alleleFrequency":0.0}],"vep":{"mostSevereConsequence":"intron_variant","transcriptConsequences":[]},"inSilicoPredictors":{"cadd":{"phred":3.252,"raw":0.211212},"pangolinLargestDs":0.0,"phylop":1.16}}
{"variantId":"X_27135703_G_T","chromosome":"X","position":27135703,"chromosomeB37":"X","positionB37":27153820,"referenceAllele":"G","alternateAllele":"T","rsIds":["rs12557104"],"alleleType":"snv","alleleFrequencies":[{"populationName":"afr_adj","alleleFrequency":0.0025361729800032515},{"populationName":"ami_adj","alleleFrequency":0.0},{"populationName":"amr_adj","alleleFrequency":0.0944471269917914},{"populationName":"asj_adj","alleleFrequency":0.0},{"populationName":"eas_adj","alleleFrequency":0.028758542141230067},{"populationName":"fin_adj","alleleFrequency":0.0},{"populationName":"mid_adj","alleleFrequency":0.0},{"populationName":"nfe_adj","alleleFrequency":3.3998828929225774E-4},{"populationName":"remaining_adj","alleleFrequency":0.021897810218978103},{"populationName":"sas_adj","alleleFrequency":0.0}],"vep":{"mostSevereConsequence":"intron_variant","transcriptConsequences":[]},"inSilicoPredictors":{"cadd":{"phred":2.706,"raw":0.162359},"pangolinLargestDs":0.0,"phylop":1.16}}
{"variantId":"X_27135724_C_T","chromosome":"X","position":27135724,"chromosomeB37":"X","positionB37":27153841,"referenceAllele":"C","alternateAllele":"T","rsIds":["rs1456640551"],"alleleType":"snv","alleleFrequencies":[{"populationName":"afr_adj","alleleFrequency":0.0},{"populationName":"ami_adj","alleleFrequency":0.0},{"populationName":"amr_adj","alleleFrequency":0.0},{"populationName":"asj_adj","alleleFrequency":0.0},{"populationName":"eas_adj","alleleFrequency":0.0},{"populationName":"fin_adj","alleleFrequency":0.0},{"populationName":"mid_adj","alleleFrequency":0.0},{"populationName":"nfe_adj","alleleFrequency":3.774724445115507E-5},{"populationName":"remaining_adj","alleleFrequency":0.0},{"populationName":"sas_adj","alleleFrequency":0.0}],"vep":{"mostSevereConsequence":"intron_variant","transcriptConsequences":[]},"inSilicoPredictors":{"cadd":{"phred":5.415,"raw":0.398941},"pangolinLargestDs":0.0,"phylop":-1.401}}
{"variantId":"X_27135725_CCT_C","chromosome":"X","position":27135725,"chromosomeB37":"X","positionB37":27153842,"referenceAllele":"CCT","alternateAllele":"C","rsIds":["rs1293174774"],"alleleType":"del","alleleFrequencies":[{"populationName":"afr_adj","alleleFrequency":0.0},{"populationName":"ami_adj","alleleFrequency":0.0},{"populationName":"amr_adj","alleleFrequency":0.0},{"populationName":"asj_adj","alleleFrequency":0.0},{"populationName":"eas_adj","alleleFrequency":0.0},{"populationName":"fin_adj","alleleFrequency":0.0},{"populationName":"mid_adj","alleleFrequency":0.0},{"populationName":"nfe_adj","alleleFrequency":5.6716135740618206E-5},{"populationName":"remaining_adj","alleleFrequency":0.0},{"populationName":"sas_adj","alleleFrequency":0.0}],"vep":{"mostSevereConsequence":"intron_variant","transcriptConsequences":[]},"inSilicoPredictors":{"cadd":{"phred":2.503,"raw":0.142979},"pangolinLargestDs":0.01,"phylop":0.982}}
{"variantId":"X_27135733_T_C","chromosome":"X","position":27135733,"chromosomeB37":"X","positionB37":27153850,"referenceAllele":"T","alternateAllele":"C","rsIds":["rs1925383031"],"alleleType":"snv","alleleFrequencies":[{"populationName":"afr_adj","alleleFrequency":3.248124208269724E-5},{"populationName":"ami_adj","alleleFrequency":0.0},{"populationName":"amr_adj","alleleFrequency":0.0},{"populationName":"asj_adj","alleleFrequency":0.0},{"populationName":"eas_adj","alleleFrequency":0.0},{"populationName":"fin_adj","alleleFrequency":0.0},{"populationName":"mid_adj","alleleFrequency":0.0},{"populationName":"nfe_adj","alleleFrequency":0.0},{"populationName":"remaining_adj","alleleFrequency":0.0},{"populationName":"sas_adj","alleleFrequency":0.0}],"vep":{"mostSevereConsequence":"intron_variant","transcriptConsequences":[]},"inSilicoPredictors":{"cadd":{"phred":7.241,"raw":0.57226},"pangolinLargestDs":0.0,"phylop":0.15}}

[buniello]

Some notes from discussions this week on the metadata section (please add/edit where relevant):

• VEP: we should add VEP most sever consequence in metadata section of the page. This is currently already in the data and we are focusing on hgvsp and impactcolumns for the transcript_consequences
• VEP: there is some discussion on whether we should also consider motif_feature_consequences and regulatory_feature_consequences
• ProtVar links: we plan to show a link-out to ProtVar (at the top of the page) when the variant is likely to be found there. If the most severe consequence is in a list of qualifying consequences (e.g. most severe consequence == “missense_variant”,…) we can build a link like this. @DSuveges to provide a list of consequences for relevant ProtVar assessment. - AI for @DSuveges to provide cross ref links from the data
• Closest gene feature: we can use current logic for now (chances are low for a variant to be too far from any gene making to the variant index) and implement a more complete solution later -- not immediate priority (expensive) - LoF curation in gnomAD (linked to an OTAR project): scoping TBD - not MVP