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Add new myvariant.info fields #1545

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kkrysiak opened this issue Nov 5, 2020 · 0 comments
Open

Add new myvariant.info fields #1545

kkrysiak opened this issue Nov 5, 2020 · 0 comments

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@kkrysiak
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kkrysiak commented Nov 5, 2020

We would like to bring in the rating and number of submitters to the MyVariant.info details box.

New pieces to bring in:
clinvar.rcv.review_status
clinvar.rcv.number_submitters

For Assertions, adding these fields to the green box displayed on Assertions would be desireable. I believe review status is higher priority than number of submitters if you have to pick.

One new concern is what happens if we link to a clinvar ID with more than one rcv. @malachig posted the following JSON which indicates there can be more than one. How are we choosing which to show? Can we show more than one in the details page and prioritize one with the highest rating or number of submitters to show in the green box on the Variant or Assertion?

"rcv": [
  {
    "accession": "RCV000252722",
    "clinical_significance": "Likely benign",
    "conditions": {
      "identifiers": {
        "medgen": "CN169374"
      },
      "name": "not specified",
      "synonyms": [
        "AllHighlyPenetrant"
      ]
    },
    "number_submitters": 1,
    "origin": "germline",
    "preferred_name": "NM_182961.4(SYNE1):c.8403C>T (p.Tyr2801=)",
    "review_status": "criteria provided, single submitter"
  },
  {
    "accession": "RCV000724249",
    "clinical_significance": "Conflicting interpretations of pathogenicity",
    "conditions": {
      "identifiers": {
        "medgen": "CN517202"
      },
      "name": "not provided"
    },
    "last_evaluated": "2019-05-29",
    "number_submitters": 2,
    "origin": "germline",
    "preferred_name": "NM_182961.4(SYNE1):c.8403C>T (p.Tyr2801=)",
    "review_status": "criteria provided, conflicting interpretations"
  }
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