{% extends "layout_bs4.html" %} {% from "utils.html" import comments_panel, pedigree_panel %} {% from "variants/utils.html" import modal_causative %} {% from "variant/variant_details.html" import old_observations %} {% from "variant/utils.html" import rankscore_panel, overlapping_panel, genes_panel, transcripts_panel, sv_alignments, pin_button, causative_button %} {% from "variant/gene_disease_relations.html" import omim_phenotypes, genemodels_panel %} {% from "variant/variant_details.html" import gtcall_panel, frequencies, observations_panel %} {% from "variant/buttons.html" import variant_tag_button, dismiss_variant_button %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }} {% endblock %} {% block css %} {{ super() }} {% endblock %} {% block top_nav %} {% endblock %} {% block top_nav_right %} {% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {% endif %} {{ super() }} {% endblock %} {% block content_main %} {% if variant.missing_data %}
Showing only first 30 genes!
{% endif %}
Basics
  • Rank {{ variant.variant_rank }}
  • Rank score {{ variant.rank_score }}
  • Category {{ variant.sub_category|upper }}
  • Gene panels:
    {% for panel_id in variant.panels %} {{ panel_id }}   {% endfor %}
    {{ variant_tag_button(variant, institute, case, manual_rank_options) }}
    {{ dismiss_variant_button(variant, institute, case, dismiss_variant_options) }}
Summary
  • Position
    {{ variant.chromosome }}:{{ variant.position }} {{ "-" if variant.end_chrom == variant.chromosome else " / " + variant.end_chrom+":" }}{{ variant.end }}
  • Breakpoint 1
    {{ sv_alignments(variant, case, "start") }}
  • Breakpoint 2
    {{ sv_alignments(variant, case, "end") }}
  • Cytoband
    {% if variant.end_chrom == variant.chromosome %} {{ variant.chromosome }}{{ variant.cytoband_start }}{{ variant.cytoband_end if variant.cytoband_end != variant.cytoband_start else "" }} {% else %} ({{ variant.chromosome + ";" + variant.end_chrom}})({{ variant.cytoband_start + ";" + variant.cytoband_end }}) {% endif %}
  • Length
    {{ sv_alignments(variant, case, "length") }}
  • Type
    {{ variant.sub_category|upper }}
  • {% if variant._id in case.suspects and not variant.clinvar_clinsig %} Submit to ClinVar {% endif %} {% if variant.clinvar_clinsig%} Modify clinvar submission {% endif %}
{{ gtcall_panel(variant) }}
{% set has_pedigree = case.madeline_info and case.individuals|length > 1 %} {% if has_pedigree %}
{{ pedigree_panel(case) }}
{% endif %}
{{ comments_panel(institute, case, current_user, variant.comments, variant_id=variant._id) }}
{{ omim_phenotypes(variant) }}
{{ frequencies(variant) }}
{% if config['LOQUSDB_SETTINGS'] %}
{{ observations_panel(variant, observations, case) }}
{{ old_observations(variant) }}
{% endif %}
{{ rankscore_panel(variant) }}
{{ overlapping_panel(variant, overlapping_vars, case, institute) }}
{{ ext_links(variant) }}
{% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {{ verify_modal() }} {% endif %} {% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {{ modal_cancel_verify() }} {% endif %} {{ modal_causative(case, institute, variant) }} {% endblock %} {% macro panel_basics() %}
Basics
{% if variant.str_repid %} {% endif %}
Position {{ variant.chromosome }}:{{ variant.position }} {% if variant.is_par %} PAR {% endif %} Change {{ variant.reference }} → {{ variant.alternative }}
Repeat locus {{variant.str_repid}}
{% for gene in variant.genes %} {% endfor %}
Gene Region Function
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {{ gene.region_annotation }} {{ gene.functional_annotation|truncate(20, True) }}
{% if cancer %}
{% endif %}
{% if not cancer %}
{% endif %} {{ acmg_form(variant.acmg_classification.code if variant.acmg_classification) }}
Classify {% if variant._id in case.suspects and not variant.clinvar_clinsig %} Submit to ClinVar {% endif %} {% if variant.clinvar_clinsig %} Modify clinvar submission {% endif %}
{% if evaluations %}
{% for evaluation in evaluations %} {{ acmg_classification_item(evaluation) }} {% endfor %}
{% endif %}
{% endmacro %} {% macro ext_links(variant) %} {# External links #}
Ensembl DECIPHER
{% endmacro %} {% macro verify_button() %} {% if variant.sanger_ordered %} {% if variant.validation in ['True positive', 'False positive']%} {% else %} {% endif %} {% else %} {% endif %} {% endmacro %} {% macro verify_modal() %}
{% endmacro %} {% macro modal_cancel_verify() %}
{% endmacro %} {% macro verify_form() %} {% endmacro %} {% block scripts %} {{ super() }} {% endblock %}