{% extends "layout.html" %} {% from "overview/institute_sidebar.html" import institute_actionbar %} {% from "clinvar/clinvar_howto.html" import clinvar_howto_modal %} {% block title %} {{ super() }} - {{ institute.display_name }} {% endblock %} {% block top_nav %} {{ super() }} {% endblock %} {% macro submissions_macro(submissions) %}

ClinVar submissions page

howto
{{ clinvar_howto_modal() }}
{% if submissions %}
{% for status in ['open', 'closed', 'submitted'] %} {% for submission in submissions|sort(attribute='status') %} {% if submission.status==status %} {{ submission_panel(submission) }} {% endif %} {% endfor %} {% endfor %}
{% else %}

No ClinVar submissions found. You can create one by choosing one or more pinned variants on a case page and clicking the button "Submit to ClinVar".

{% endif %}
{% endmacro %} {% macro submission_panel(subm_obj) %}

{% if subm_obj.status == 'open' and show_submit %} {{ submit_modal(subm_obj) }} {% endif %}

Variant data:

{% if subm_obj.variant_data and subm_obj.variant_data | length > 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.var_type, subm_variant.chromosome, subm_variant.breakpoint1 or subm_variant.outer_start or ""]) }) %} {% else %} {% if subm_variant.ref_seq and subm_variant.hgvs %} {% do var_key_name.update( {subm_variant.local_id : '_'.join([subm_variant.ref_seq, subm_variant.hgvs])} ) %} {% 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 %} {% endif %} {% endfor %}
Name Type Case Refseq Gene HGVS Significance Added by
{{loop.index}} {{var_key_name[subm_variant.local_id]|truncate(25,true,'..')}}
SV
{{var_key_name[subm_variant.local_id]|truncate(25,true,'..')}}
SNV
{{subm_obj.cases[subm_variant.case_id]}} {{subm_variant.ref_seq or '-'}} {{subm_variant.gene_symbol or '-'}} {{subm_variant.hgvs|truncate(25,true,'..') or '-'}} {{subm_variant.clinsig}} {{subm_variant.added_by or "N/A"}}
{% else %}

This submission is open but has no variants yet.

{% endif %}
{% if subm_obj.case_data and subm_obj.case_data | length > 0 %}

Observation data:

{% for case in subm_obj.case_data %} {% endfor %}
Individual ID Case ID Variant Allele origin
{{loop.index}}
{{subm_obj.cases[case.case_id]}} {{var_key_name[case.linking_id]|truncate(25,true,'..')}} {{case.allele_origin}}
{% else %}

No case data provided for the above variants

{% endif %}
{% endmacro %} {% macro submit_modal(subm_obj) %} {% endmacro %} {% block content_main %}
{{ institute_actionbar(institute, "shared") }}
{{ submissions_macro(submissions) }}
{% endblock %} {% block scripts %} {{ super() }} {% endblock %}