{% macro variant_gene_symbols_cell(variant) %}
{% if variant.hgnc_symbols|length >= 5 %} {{ variant.hgnc_symbols|length }}
{% for symbol in variant.hgnc_symbols|sort %} {{symbol}}
{% endfor %}
{% else %}
{% if variant.hgnc_symbols %} {{ variant.hgnc_symbols|length }} {% endif %} {{variant.hgnc_symbols|sort|join(", ")}}
{% endif %}
{% endmacro %} {% macro fusion_variant_gene_symbols_cell(variant) %}
{% if variant.genes %} {% for gene in variant.genes %} {{ gene.hgnc_symbol or gene.hgnc_id }}
{% endfor %} {% else %} {% for symbol in variant.fusion_genes %} {{ symbol }}
{% endfor %} {% endif %}
{% endmacro %} {% macro variant_funct_anno_cell(variant) %}
{% if variant.category == "fusion" %} {{ variant.frame_status|lower if variant.frame_status else "-" }} {% else %} {% if variant.functional_annotations|length >= 5 %}
{% for annotation in variant.functional_annotations|sort %} {{ annotation|replace("_", " ") }}
{% endfor %}
{% else %}
{{ variant.functional_annotations|sort|join(", ")|replace("_", " ") }}
{% endif %} {% endif %}
{% endmacro %} {% macro variant_region_anno_cell(variant) %}
{% if variant.functional_annotations|length >= 5 %}
{% for annotation in variant.region_annotations|sort %} {{ annotation }}
{% endfor %}
{% else %}
{{ variant.region_annotations|sort|join(", ") }}
{% endif %}
{% endmacro %} {% macro gene_cell(variant) %}
{% if variant.category == "cancer" or variant.category == "sv_cancer" %} {{ variant.first_rep_gene.hgnc_symbol or variant.first_rep_gene.hgnc_id }} {% if variant.secondary_gene %} ({{ variant.second_rep_gene.hgnc_symbol or variant.second_rep_gene.hgnc_id }}) {% endif %} {% set panel_count = variant.case_panels|rejectattr('removed')|list|length %} {% if panel_count > 0%} {{panel_count}} {% endif %} {% else %} {% for gene in variant.genes %} {{ gene.hgnc_symbol or gene.hgnc_id }} {% endfor %} {% set panel_count = variant.case_panels|rejectattr('removed')|list|count %} {% if panel_count > 0 %} {{panel_count}} {% endif %} {% endif %}
{% endmacro %} {% macro observed_cell_general(variant) %}
{% if variant.clinsig_human %} ClinVar
{% endif%} {% if variant.cosmic_ids %} COSMIC
{% endif %} {% if variant.mitomap_associated_diseases %} MITOMAP
{% endif %} {% if variant.clingen_cgh_pathogenic %} CGH Pathogenic
{% endif %} {% if variant.local_obs_old or variant.local_obs_cancer_germline_old or variant.local_obs_cancer_somatic_old %} Local
{% endif %}
{% endmacro %} {% macro frequency_cell_general(variant) %}
{% if variant.category == "mei" %} {{ variant.swegen_mei_max|human_decimal if variant.swegen_mei_max else '~' }} {% elif variant.chromosome != "MT" %} {{ variant.gnomad_frequency|human_decimal if variant.gnomad_frequency else '~' }} {% else %} {{ variant.gnomad_mt_homoplasmic_frequency|human_decimal if variant.gnomad_mt_homoplasmic_frequency else '~' }} {% endif %}
{% endmacro %} {% macro external_stylesheets() %} {% endmacro %} {% macro external_scripts() %} {% endmacro %}