{% extends "layout_bs4.html" %} {% from "utils.html" import comments_panel, activity_panel, pedigree_panel %} {% from "variants/utils.html" import compounds_table, modal_causative %} {% from "variant/utils.html" import rankscore_panel, overlapping_panel, genes_panel, transcripts_panel, proteins_panel, pin_button, causative_button %} {% from "variant/tx_overview.html" import disease_associated, transcripts_overview %} {% from "variant/gene_disease_relations.html" import omim_phenotypes, inheritance_panel, autozygosity_panel, genemodels_panel %} {% from "variant/variant_details.html" import frequencies, gtcall_panel, observations_panel, old_observations, severity_list, conservations, mappability %} {% from "variant/buttons.html" import variant_tag_button, variant_tier_button, dismiss_variant_button, mosaic_variant_button %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }} {% endblock %} {% block css %} {{ super() }} {% 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() }}
{{ panel_basics() }}
{{ panel_summary() }}
{% if variant.disease_associated_transcripts %}
{{ disease_associated(variant) }}
{% endif %}
{{ transcripts_overview(variant) }}
{{ inheritance_panel(variant) }}
{% if variant.azlength %}
{{ autozygosity_panel(variant) }}
{% endif %}
{{ genemodels_panel(variant) }}
{{ omim_phenotypes(variant) }}
{{ frequencies(variant) }}
{% if config['LOQUSDB_SETTINGS'] %}
{{ observations_panel(variant, observations, case) }}
{% endif %}
{{ old_observations(variant) }}
{{ severity_list(variant) }}
{{ conservations(variant) }}
{{ mappability(variant) }}
{{ comments_panel(institute, case, current_user, variant.comments, variant_id=variant._id) }}
{{ gtcall_panel(variant) }}
{% set has_pedigree = case.madeline_info and case.individuals|length > 1 %} {% if has_pedigree %}
{{ pedigree_panel(case) }}
{% endif %}
{% if variant.compounds %}
{{ compounds_panel() }}
{% endif %}
{{ rankscore_panel(variant) }}
{{ overlapping_panel(variant, overlapping_vars, case, institute) }}
{{ external_links() }}
{{ activity_panel(events|reverse) }}
{% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {{ modal_sanger() }} {% endif %} {% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {{ modal_cancel_sanger() }} {% endif %} {{ modal_causative(case, institute, variant) }} {% endblock %} {% macro sanger_button() %} {% if variant.sanger_ordered %} {% if variant.validation in ['True positive', 'False positive']%} {% else %} {% endif %} {% else %} {% endif %} {% endmacro %} {% macro sanger_form() %} {% endmacro %} {% macro matching_variants() %}
{% if causatives %}
Matching causatives from other cases
{% else %}
No matching causative variants
{% endif%}
{% endmacro %} {% macro panel_basics() %}
Basics
{% if variant.str_repid %} {% endif %}
Position {{ variant.chromosome }}:{{ variant.position }} {% if variant.is_par %} PAR {% endif %} 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 -%}
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) }}
{{ variant_tag_button(variant, institute, case, manual_rank_options) }} {% if cancer %} {{ variant_tier_button(variant, institute, case, cancer_tier_options) }} {% endif %} {{ dismiss_variant_button(variant, institute, case, dismiss_variant_options) }} {% if not cancer %} {{ mosaic_variant_button(variant, institute, case, mosaic_variant_options) }} {% 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 panel_summary() %}
Summary
Rank {{ variant.variant_rank }} Rank score {{ variant.rank_score }} CADD score {{ variant.cadd_score or '-' }}
Matches OMIM inhert. {% if variant.is_matching_inheritance %} Yes {% else %}
No
{% endif %}
Frequency
{{ variant.frequency }}
{% if variant.clinsig_human %} {% for clinsig in variant.clinsig_human %} {% else %} No annotations {% endfor %}
CLINSIG Accession Revstat
{{ clinsig.human }} {{ clinsig.accession }} {{ clinsig.revstat }}
{% endif %}
{% if case.mt_bams or case.bam_files %} {% endif %}
Gene coverage
{% if config.SQLALCHEMY_DATABASE_URI %} {% for gene in variant.genes %} {% endfor %} {% endif %}
{% if variant.chromosome == "MT" %} {% if case.mt_bams %} {% else %} MT BAM file(s) missing {% endif %} {% elif case.bam_files %} {% if case.rhocall_beds %} {% endif %} {% if case.tiddit_coverage_wigs %} {% endif %} {% if case.upd_regions_beds %} {% endif %} {% if case.upd_sites_beds %} {% endif %} {% else %} BAM file(s) missing {% endif %} {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
{% if variant.custom %} {% for pair in variant.custom %} {% endfor %}
Custom annotation Value
{{ pair[0] }} {{ pair[1] }}
{% endif %}
{% endmacro %} {% macro compounds_panel() %}
Compounds (top 20)
{{ compounds_table(institute, case, variant.compounds[:20]) }}
{% endmacro %} {% macro modal_sanger() %}
{% endmacro %} {% macro modal_cancel_sanger() %}
{% endmacro %} {% macro external_links() %}
{% for gene in variant.genes %}
External links: {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
Ensembl HPA STRING GENEMANIA UCSC {% if gene.entrez_link %} Entrez {% endif %} SPANR Reactome Expr. Atlas ClinGen {% if case.mt_bams or case.bam_files %} Alamut {% endif %} Protein Paint {% if variant.chromosome == 'MT' %} MitoMap {% endif %}
{% endfor %}
{% endmacro %} {% macro acmg_form(selected=None) %}
{% for option in ACMG_OPTIONS %} {% endfor %}
{% endmacro %} {% macro acmg_classification_item(data) %} {% set current_variant = (data.variant_specific == variant._id) %}
  • {{ data.classification.label }} {{ data.classification.short }} {% if not current_variant %} {{ data.case.display_name }} {% endif %}
    {{ data.user_name }} on {{ data.created_at.date() }} {% if current_variant %} {% endif %}
  • {% endmacro %} {% block scripts %} {{ super() }} {% endblock %}