{% extends "layout.html" %} {% from "variants/utils.html" import compounds_table, svs_table %} {% from "variants/components.html" import gene_cell, frequency_cell %} {% from "utils.html" import flash_messages, comments_table %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ form.variant_type.data|capitalize }} variants {% endblock %} {% block top_nav %} {{ super() }}
  • Institutes
  • {{ institute.display_name }}
  • {{ case.display_name }}
  • {{ form.variant_type.data|capitalize }} SNV and INDELs
  • {% endblock %} {% block top_nav_right %}
  • {{ super() }} {% endblock %} {% block content %}
    {{ filters_form() }}
    {{ flash_messages() }}
    {% for variant in variants %} {% if variant.dismiss_variant %} {% else %} {% endif %} {% else %} {% endfor %}
    Rank Score Chr. Gene PopFreq CADD Gene annotation Func. annotation Inheritance model Overlapping
    {{ cell_rank(variant) }} {{ variant.rank_score|int }} {{ variant.chromosome }} {{ gene_cell(variant) }} {{ frequency_cell(variant) }} {{ cell_cadd(variant) }} {% for annotation in variant.region_annotations %}
    {{ annotation }}
    {% endfor %}
    {% for annotation in variant.functional_annotations %}
    {{ annotation }}
    {% endfor %}
    {{ cell_models(variant) }} {{ overlapping_cell(variant) }}
    No matching variants
    {{ footer() }}
    {% endblock %} {% macro cell_rank(variant) %} {{ variant.variant_rank }} {% set comment_count = variant.comments.count() %} {% if variant.acmg_classification %} {{ variant.acmg_classification.short }} {% elif variant.manual_rank %} {{ variant.manual_rank }} {% elif variant.evaluations %} {% for evaluation in (variant.evaluations or []) %} {{ evaluation.classification.short }} {% endfor %} {% endif %} {% if comment_count > 0 %} {% set comments_content = comments_table(institute, case, variant.comments, variant._id) %} {{ comment_count }} {% if 'GLOBAL' in comments_content %} {% endif %} {% endif %} {% if variant._id in case.suspects %} {% endif %} {% endmacro %} {% macro cell_cadd(variant) %}
    {{ variant.cadd_score }}
    {% endmacro %} {% macro cell_models(variant) %} {% for model in (variant.genetic_models or []) %}
    {{ model }}
    {% endfor %} {% if variant.compounds %} Compounds {% endif %} {% if variant.mosaic_tags %} mosaic {% endif %} {% endmacro %} {% macro overlapping_cell(variant) %} {% if variant.overlapping %} Overlapping SVs {% else %} - {% endif %} {% endmacro %} {% macro footer() %}
    {% if more_variants %}
    {% else %} No more variants to display {% endif %}
    {% endmacro %} {% macro filters_form() %} {{ form.csrf_token }} {{ form.variant_type() }}
    {{ form.gene_panels.label(class="control-label") }} {{ form.gene_panels(class="form-control") }}
    {{ form.symbol_file.label(class="control-label") }} {{ form.symbol_file(class="form-control") }}
    {{ form.region_annotations.label(class="control-label") }} {{ form.region_annotations(class="form-control") }}
    {{ form.functional_annotations.label(class="control-label") }} {{ form.functional_annotations(class="form-control") }}
    {{ form.genetic_models.label(class="control-label") }} {{ form.genetic_models(class="form-control") }}
    {{ form.hgnc_symbols.label(class="control-label") }} {{ form.hgnc_symbols(class="form-control") }}
    {{ form.cadd_score.label(class="control-label") }} {{ form.cadd_score(class="form-control") }}
    {{ form.cadd_inclusive.label(class="control-label") }}
    {{ form.cadd_inclusive() }}
    {{ form.clinsig.label(class="control-label") }} {{ form.clinsig(class="form-control") }}
    {{ form.clinsig_confident_always_returned.label(class="control-label") }}
    {{ form.clinsig_confident_always_returned() }}
    {{ form.spidex_human.label(class="control-label") }} {{ form.spidex_human(class="form-control") }}
    {{ form.gnomad_frequency.label(class="control-label") }} {{ form.gnomad_frequency(class="form-control") }}
    {{ form.local_obs.label(class="control-label") }} {{ form.local_obs(class="form-control") }}
    {{ form.chrom.label(class="control-label") }} {{ form.chrom(class="form-control") }}
    {{ form.filter_variants(class_="btn btn-primary form-control") }}
    {{ form.clinical_filter(class_="btn btn-default form-control") }}
    {{ form.export(class_="btn btn-warning form-control") }}
    {% endmacro %} {% block scripts %} {{ super() }} {% endblock %}