{% from "variant/buttons.html" import variant_tag_button, variant_tier_button, dismiss_variant_button, mosaic_variant_button %} {% from "variants/utils.html" import compounds_table %} {% from "variant/variant_details.html" import severity_list %} {% from "variant/buttons.html" import reviewer_button, splice_junctions_button %} {% from "variant/utils.html" import igv_track_selection %} {% macro clinsig_table(variant) %} {% if variant.clinsig_human %} {% for clinsig in variant.clinsig_human %} {% if clinsig.accession %} {% else %} {% endif %} {% else %} No annotations {% endfor %}
CLINSIG Accession Revstat
{{ clinsig.human }}{{ clinsig.accession }}n.a.
{{ clinsig.revstat or "n.a." }}
{% endif %} {% endmacro %} {% macro acmg_classification_item(variant, 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 %} {% macro alignments(institute, case, variant, current_user, config, igv_tracks, has_rna_tracks=False) %} {% endmacro %} {% macro acmg_form(institute, case, variant, ACMG_OPTIONS, selected=None) %}
    {% for option in ACMG_OPTIONS %} {% endfor %}
    {% endmacro %} {% macro panel_classify(variant, institute, case, ACMG_OPTIONS, manual_rank_options, cancer_tier_options, dismiss_variant_options, mosaic_variant_options, evaluations) %}
    Classify
    {{ variant_tag_button(variant, institute, case, manual_rank_options) }} {% if case.track == "cancer" %} {{ variant_tier_button(variant, institute, case, cancer_tier_options) }} {% endif %} {{ dismiss_variant_button(variant, institute, case, dismiss_variant_options) }} {% if case.track != "cancer" %} {{ mosaic_variant_button(variant, institute, case, mosaic_variant_options) }} {% endif %} {{ acmg_form(institute, case, variant, ACMG_OPTIONS, variant.acmg_classification.code if variant.acmg_classification) }} {% if evaluations %}
    {% for evaluation in evaluations %} {{ acmg_classification_item(variant, evaluation) }} {% endfor %}
    {% endif %}
    {% endmacro %} {% macro matching_variants(managed_variant, causatives, matching_manual_ranked=None, matching_tiered=None) %} {% if causatives %}
    Matching causatives from other cases:  {% for other_variant in causatives %} {{ other_variant.case_display_name }}   {% if other_variant.partial %} partial {% endif %} {% endfor %}
    {% endif %} {% if managed_variant %}
    Matching managed variant:
    {{ managed_variant.display_id }}
    {{ managed_variant.description }}
    {% endif %} {% if not managed_variant and not causatives %}
    No matching causative or managed variants
    {% endif %} {% if matching_manual_ranked %}
    Matching manually ranked variants:  {% for manual_rank, manual_rank_info in matching_manual_ranked.items() %}
    {{manual_rank_info.label}}: {% for link in manual_rank_info["links"] %} {% set match_case = link.split('/') %} {{match_case[4]}}  {% endfor %}
    {% endfor %}
    {% endif %} {% if matching_tiered %}
    Matching tiered:  {% for tier, tiered_info in matching_tiered.items() %}
    {{tier}}: {% for link in tiered_info["links"] %} {% set match_case = link.split('/') %} {{match_case[4]}}  {% endfor %}
    {% endfor %}
    {% endif %} {% endmacro %} {% macro compounds_panel(institute, case, variant) %}
    Compounds (top 20)
    {{ compounds_table(institute, case, variant.compounds[:20]) }}
    {% endmacro %} {% macro external_links(case, variant, cancer, str) %}
    {% 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 %} {% if gene.pubmed_link %} PubMed {% endif %} {% if gene.decipher_link %} Decipher {% endif %} SPANR Reactome Expr. Atlas ClinGen GenCC Protein Paint {% if variant.is_mitochondrial %} MitoMap {% endif %} {% if variant.hmtvar_variant_id %} HmtVar {% endif %} {% if gene.tp53_link %} MutanTP53 {% endif %} {% if gene.iarctp53_link %} TP53 Database {% endif %} {% if cancer %} cBioPortal OncoKB CIViC CKB {% endif %} {% if str %} STRipy GnomAD STR {% endif %} PanelApp MARRVEL
    {% endfor %}
    {% endmacro %} {% macro external_stylesheets() %} {% endmacro %} {% macro external_scripts() %} {% endmacro %} {% macro variant_scripts() %} {% endmacro %}