{% extends "layout_bs4.html" %} {% block title %} {{ super() }} - {{ institute.display_name }} {% endblock %} {% block top_nav %} {{ super() }} {% if config.SHOW_CAUSATIVES %} {% endif %} {% 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) %}
Submission {{subm_obj._id}} - ({{subm_obj.status|upper}}) / Created: {{subm_obj.created_at.strftime('%Y-%m-%d')}} / Last updated: {{subm_obj.updated_at.strftime('%Y-%m-%d')}}

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 %}