{% extends "bootstrap_global.html" %} {% block css %} {{ super() }} {% endblock %} {% block head %} {{ super() }} {% endblock head %} {% block content %} {% if variant_data.var_obj.category in ["snv", "cancer"]%} {% set var_category = 'snv' %} {% else %} {% set var_category = 'sv' %} {% endif %}
  • Start
  • Assertion Criteria
  • Variant Details
  • Inheritance Model
  • Clinical Significance
  • Associated conditions
  • Observation Data
ClinVar variant submission form

The form present on this page mirrors the fields on the ClinVar submission spreadsheets.
After collecting the required fields, this variant gets saved in an open ClinVar submission object.

Assertion criteria ? {{ variant_data.var_form.csrf_token }} {{ variant_data.var_form.case_id() }} {{ variant_data.var_form.category() }} {{ variant_data.var_form.local_id() }} {{ variant_data.var_form.linking_id() }} {{ variant_data.var_form.ref() }} {{ variant_data.var_form.alt() }} {% if var_category == 'snv' %} {{ variant_data.var_form.chromosome() }} {{ variant_data.var_form.start() }} {{ variant_data.var_form.stop() }} {% endif %}

{{variant_data.var_form.last_evaluated.label(class="fw-bold text-dark")}} {{variant_data.var_form.last_evaluated(class="bg-white")}}

{{variant_data.var_form.assertion_method.label(class="fw-bold text-dark")}} {{variant_data.var_form.assertion_method(class="bg-white")}}

{{variant_data.var_form.assertion_method_cit.label(class="fw-bold text-dark")}} {{variant_data.var_form.assertion_method_cit(class="bg-white")}}
Variant Details {{variant_data.var_form.gene_symbol.label(class="fw-bold, text-dark")}} ? {{variant_data.var_form.gene_symbol(class="bg-white")}}
{% if var_category == 'snv' %}

{{variant_data.var_form.tx_hgvs.label(class="fw-bold, text-dark")}} ? VariantValidator

{% with messages = get_flashed_messages() %} {% if messages %} {% for message in messages %} {{ message }}
{% endfor %}

{% endif %} {% endwith %} {% set ns = namespace(label='', validated=false) %} {% for item_row in variant_data.var_form.tx_hgvs | batch(3) %} {% for item in item_row %} {% if "(validated)" in item.label.text %} {% set ns.validated = true %} {% else %} {% set ns.validated = false %} {% endif %} {% set ns.label = item.label.text | replace(" (validated)", "") %} {% endfor %} {% endfor %}
{{item()}}

25 %} data-bs-toggle="tooltip" title="{{ns.label}}">{{ ns.label|truncate(25,true,'..') }} {% else %} >{{ ns.label }} {% endif %} {% if ns.validated %} {% endif %}



{{variant_data.var_form.variations_ids.label(class="fw-bold, text-dark")}} {{variant_data.var_form.variations_ids(class="bg-white")}}
{% else %}
{{variant_data.var_form.var_type.label(class="fw-bold, text-dark")}} {{variant_data.var_form.var_type(class="form-control, btn-secondary")}}

{{variant_data.var_form.ref_copy.label(class="fw-bold, text-dark")}} {{variant_data.var_form.ref_copy(size=5, class="bg-white")}}

{{variant_data.var_form.ncopy.label(class="fw-bold, text-dark")}} ? {{variant_data.var_form.ncopy(size=5, class="bg-white")}}

{{variant_data.var_form.chromosome.label(class="fw-bold, text-dark")}} {{variant_data.var_form.chromosome(size=5, class="bg-white")}}

{{variant_data.var_form.breakpoint1.label(class="fw-bold, text-dark")}} {{variant_data.var_form.breakpoint1(class="bg-white")}}

{{variant_data.var_form.breakpoint2.label(class="fw-bold, text-dark")}} {{variant_data.var_form.breakpoint2(class="bg-white")}}

{{variant_data.var_form.outer_start.label(class="fw-bold, text-dark")}} {{variant_data.var_form.outer_start(size=20, class="bg-white")}}

{{variant_data.var_form.inner_start.label(class="fw-bold, text-dark")}} {{variant_data.var_form.inner_start(size=20, class="bg-white")}}

{{variant_data.var_form.inner_stop.label(class="fw-bold, text-dark")}} {{variant_data.var_form.inner_stop(size=20, class="bg-white")}}

{{variant_data.var_form.outer_stop.label(class="fw-bold, text-dark")}} {{variant_data.var_form.outer_stop(size=20, class="bg-white")}}
{% endif %}
Inheritance model

The mode of inheritance specific to the variant-disease pair, not generally for the disease

{{variant_data.var_form.inheritance_mode.label(class="fw-bold, text-dark")}} {{variant_data.var_form.inheritance_mode(class="form-control, btn-secondary")}}
Clinical Significance

The interpretation, or clinical significance, of the variant for the submitted condition

Classification in Scout:
{{variant_data.var_obj.classification|replace("_"," ")|upper if variant_data.var_obj.classification else "n.a."}}
{{variant_data.var_form.clinsig.label(class="fw-bold, text-dark")}} * {{variant_data.var_form.clinsig(class="form-control, btn-secondary")}}



{{variant_data.var_form.clinsig_comment.label(class="fw-bold, text-dark")}} ? {{variant_data.var_form.clinsig_comment(class="form-control, bg-white", placeholder="(optional)")}}

{{variant_data.var_form.clinsig_cit.label(class="fw-bold, text-dark")}} {{variant_data.var_form.clinsig_cit(class="form-control, bg-white", placeholder="(optional) e.g. PMID:123456, PMCID:PMC3385229, NBK:56955")}}
Associated Conditions

The condition for which the variant is interpreted. Examples available at ClinVar"

{{variant_data.var_form.condition_type.label(class="fw-bold, text-dark")}}*

{{variant_data.var_form.conditions.label(class="fw-bold, text-dark")}} *?
{{variant_data.var_form.omim_terms.label(class="fw-bold, text-dark")}}
    {% for term in variant_data.var_form.omim_terms %}
  • {{ term.label }}
  • {% else %} n.a. {% endfor %}


{{variant_data.var_form.hpo_terms.label(class="fw-bold, text-dark")}}
    {% for term in variant_data.var_form.hpo_terms %}
  • {{ term.label }}
  • {% else %} n.a.
{% endfor %}
Observation Data

Information provided by filling in these fields will be used to create the CaseData.csv file. Observations from at least one individuals are required.

    {% for cdata in variant_data.cdata_forms %} {{cdata.linking_id(class="fw-bold, text-dark")}}
  • {{ cdata.include_ind.label(class="fw-bold, text-dark") }} {{ cdata.include_ind() }}
    {{ cdata.individual_id.label(class="fw-bold, text-dark") }} {{ cdata.individual_id(class="form-control, bg-white", readonly=true) }}
    {{ cdata.affected_status.label(class="fw-bold, text-dark") }} {{ cdata.affected_status(class="form-control, btn-secondary") }}
    {{ cdata.allele_of_origin.label(class="fw-bold, text-dark") }} {{ cdata.allele_of_origin(class="form-control, btn-secondary") }}
    {{ cdata.collection_method.label(class="fw-bold, text-dark") }} {{ cdata.collection_method(class="form-control, btn-secondary") }}
  • {% endfor %}
{% endblock %} {% block scripts %} {{ super() }} {% endblock %}