{% extends "layout.html" %} {% block title %} {{ super() }} - {{ institute_id }} {% endblock %} {% block top_nav %} {{ super() }}
  • Institutes
  • {{ institute_id }} Cases
  • {% if config.SHOW_CAUSATIVES %}
  • Causatives
  • {% endif %}
  • All SNVs and INDELs
  • Clinvar submissions
  • {% endblock %} {% block content_main %}

    Clinvar submissions page

    howto

    {% if submissions %} {% for submission in submissions|sort(attribute='status', reverse=True) %} {{ submission_panel(submission) }} {% endfor %} {% else %}

    No clinvar submission was found. You can create one by clicking on "Submit to Clinvar" from the page of a pinned variant.

    {% endif %}
    {% endblock %} {% macro submission_panel(subm_obj) %}
    {% if subm_obj.status=='open' %}
    {% else %}
    {% endif %}
    Submission {{subm_obj._id}} - ({{subm_obj.status|upper}})

    Variant data:

    {% if subm_obj.variant_data and subm_obj.variant_data.count() > 0 %} {% set var_key_name = {} %} {% for subm_variant in subm_obj.variant_data %} {% if subm_variant.category == 'sv' %} {% do var_key_name.update( {subm_variant.local_id : '_'.join([subm_variant.chromosome, subm_variant.breakpoint1, subm_variant.ref[0:5], subm_variant.alt[0:5]]) }) %} {% else %} {% do var_key_name.update( {subm_variant.local_id : '_'.join([subm_variant.chromosome, subm_variant.start, subm_variant.ref[0:5], subm_variant.alt[0:5]]) }) %} {% endif %} {% endfor %}
    ID Type Case Refseq HGVS Significance
    {{loop.index}} {{var_key_name[subm_variant.local_id]}}
    SV
    {{var_key_name[subm_variant.local_id]}}
    SNV
    {{subm_variant.case_id}} {{subm_variant.ref_seq or '-'}} {{subm_variant.hgvs or '-'}} {{subm_variant.clinsig}}
    {% else %}

    This submission is open but has no variants yet.

    {% endif %}

    Case data:

    {% if subm_obj.case_data and subm_obj.case_data.count() > 0 %} {% for case in subm_obj.case_data %} {% endfor %}
    Individual ID Case ID Clinical features Variant ID Allele origin
    {{loop.index}} {{case.individual_id}} {{case.case_id}} {{case.clin_features}} {{var_key_name[case.linking_id]}} {{case.allele_origin}}
    {% else %}

    No case data provided for the above variants

    {% endif %}
    {% endmacro %} {% block scripts %} {% endblock %}