{% extends "layout.html" %} {% from "variant/buttons.html" import database_buttons %} {% from "utils.html" import activity_panel, comments_panel, pedigree_panel %} {% from "variants/utils.html" import compounds_table %} {% from "variant/utils.html" import causative_button, genes_panel, modal_causative, overlapping_panel, pin_button, proteins_panel, transcripts_panel %} {% from "variant/tx_overview.html" import disease_associated, transcripts_overview %} {% from "variant/gene_disease_relations.html" import autozygosity_panel, genemodels_panel, inheritance_panel, omim_phenotypes %} {% from "variant/variant_details.html" import frequencies, gtcall_panel, old_observations, observations_panel, severity_list, conservations, mappability %} {% from "variant/components.html" import alignments, clinsig_table, compounds_panel, external_links, external_scripts, external_stylesheets, matching_variants, panel_classify, variant_scripts %} {% from "variant/sanger.html" import modal_cancel_sanger, modal_sanger, sanger_button %} {% from "variant/rank_score_results.html" import rankscore_panel %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }} {% endblock %} {% block css %} {{ super() }} {{ external_stylesheets() }} {% endblock %} {% block top_nav %} {{ super() }} {% 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 %}
{{ matching_variants(managed_variant, causatives, variant.matching_ranked) }}
{{ panel_classify(variant, institute, case, ACMG_OPTIONS, manual_rank_options, cancer_tier_options, dismiss_variant_options, mosaic_variant_options, evaluations) }}
{{ panel_summary() }}
{{ frequencies(variant) }} {% if config['LOQUSDB_SETTINGS'] %} {{ observations_panel(variant, observations, case) }} {% endif %} {{ old_observations(variant) }}
{{ comments_panel(institute, case, current_user, variant.comments, variant_id=variant._id) }}
{{ omim_phenotypes(variant) }} {{ genemodels_panel(variant, inherit_palette) }} {{ inheritance_panel(variant) }}
{% if variant.disease_associated_transcripts %}
{{ disease_associated(variant) }}
{% endif %}
{{ transcripts_overview(variant) }}
{% set has_pedigree = case.madeline_info and case.individuals|length > 1 %} {% if has_pedigree %}
{{ pedigree_panel(case) }}
{% endif %}
{{ gtcall_panel(variant) }}
{{ severity_list(variant) }}
{{ conservations(variant) }}
{% if variant.azlength %}
{{ autozygosity_panel(variant) }}
{% endif %}
{{ mappability(variant) }}
{% if variant.compounds %}
{{ compounds_panel(institute, case, variant) }}
{% endif %} {{ rankscore_panel(rank_score_results) }}
{{ overlapping_panel(variant, overlapping_vars, case, institute) }}
{{ external_links(case, variant, cancer, str) }}
{% if variant.custom_images %}
{{ panel_custom_images(variant.custom_images) }}
{% endif %}
{{ activity_panel(events|reverse) }}
{% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {{ modal_sanger(institute, case, variant, current_user) }} {% endif %} {% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {{ modal_cancel_sanger(institute, case, variant, current_user) }} {% endif %} {{ modal_causative(case, institute, variant) }} {% endblock %} {% macro panel_custom_images(images) %}
{% for image in images %}
{{ image.title }}
{% endfor %}
{% endmacro %} {% macro panel_summary() %}
Summary
Position: {{ variant.chromosome }}:{{ variant.position }} Change: {% if variant.reference|length > 8 %} {{ variant.reference[:1] }}..{{variant.reference[-1:]}} {% else %} {{ variant.reference }} {% endif %} → {%- if variant.alternative|length > 8 -%} {{ variant.alternative[:1] }}..{{variant.alternative[-1:]}} {% else %} {{ variant.alternative }} {% endif %}
Rank {{ variant.variant_rank }} Rank score {{ variant.rank_score }} CADD score {% if variant.cadd_score %} {{ variant.cadd_score|round(1) }} {% else %} - {% endif %} QUAL {% if variant.quality %} {{ variant.quality|int }} {% else %} - {% endif %}
Matches OMIM inhert. {% if variant.is_matching_inheritance %} Yes {% else %}
No
{% endif %}
Frequency
{{ variant.frequency }}
{{ clinsig_table(variant) }} {% if variant.mitomap_associated_diseases %}
MITOMAP associated diseases {{ variant.mitomap_associated_diseases.split('/')|join('
')|safe }}
{% endif %} {% 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 variant.category != "str" %} {{ database_buttons(variant) }} {% endif %} {{ alignments(institute, case, variant, current_user, config, igv_tracks, has_rna_tracks) }} {% if variant.custom %} {% for pair in variant.custom %} {% endfor %}
Custom annotation Value
{{ pair[0] }} {{ pair[1] }}
{% endif %}
{% endmacro %} {% block scripts %} {{ super() }} {{ external_scripts() }} {{ variant_scripts() }} {% endblock %}