{% from "variant/gene_disease_relations.html" import incomplete_penetrance_badge, inheritance_badge %}
{% from "variants/utils.html" import compounds_table, overlapping_tooltip_table %}
{% macro variant_gene_symbols_cell(variant, inherit_palette) %}
{% if variant.hgnc_symbols|length >= 5 %}
{{ variant.hgnc_symbols|length }}
[...]
{% for symbol in variant.hgnc_symbols|sort %}
{{symbol}}
{% else %}
{% endif %}
{% endmacro %}
{% macro fusion_variants_header() %}
Rank (beta)
Fusion Genes
Callers
Observed
Score (beta)
Junction Reads
Split Reads
FFPM
Frame Status
Transcript ID
Exon Number
Breakpoints
Orientation
{% endmacro %}
{% macro default_fusion_variant_cells(institute, case, variant) %}
{{ fusion_variant_gene_symbols_cell(variant) }}
{{ variant.tool_hits|int if variant.tool_hits else "-" }} {{variant.found_db|join(", ") if variant.found_db else "-"}}
{{ variant.fusion_score|float|round(3) if variant.fusion_score else "-" }}
{{ variant.samples[0].read_depth }}
{{ variant.samples[0].split_read }}
{{ variant.samples[0].ffpm }}
{{ variant.frame_status }}
{% if variant.genes %}
{% for gene in variant.genes %}
{% for transcript in gene.transcripts %}
{{ transcript.transcript_id }}
{% endfor %}
{% endfor %}
{% endif %}
{% if variant.genes %}
{% for gene in variant.genes %}
{% for transcript in gene.transcripts %}
{% if "exon" in transcript %}{{ transcript.exon|int }}{% endif %}
{% endfor %}
{% endfor %}
{% endif %}
{{ variant.chromosome }}:{{ variant.position }}
{{ variant.orientation }}
{% endmacro %}
{% macro fusion_variant_gene_symbols_cell(variant) %}
{% if variant.genes %}
{% for gene in variant.genes %}
{{ gene.hgnc_symbol or gene.hgnc_id }}
{% endfor %}
{% endif %}
{% for symbol in variant.fusion_genes %}
{% if symbol not in variant.hgnc_symbols %}
{{ symbol }}
{% endif %}
{% endfor %}
{% if variant.category == "fusion" %}
{{ variant.frame_status|lower if variant.frame_status else "-" }}
{% else %}
{% if variant.functional_annotations|length >= 5 %}
{% if variant.missing_data %}[first 30 genes]{% else %}[...]{% endif %}
{% for annotation in variant.functional_annotations|sort %}
{{ annotation|replace("_", " ") }}
{% else %}
{{ variant.functional_annotations|sort|join(", ")|replace("_", " ") }}
{% endif %}
{% endif %}
{% endmacro %}
{% macro gene_tooltip(gene) %}
{{ gene.hgnc_symbol }} : {{ gene.description }}
{% if gene.inheritance %}
Models : {{ gene.inheritance|join(',') }}
{% endif %}
{% if gene.incomplete_penetrance %}
Incomplete penetrance (HPO)
{% endif %}
{% if gene.phenotypes %}
OMIM disease
{% for disease in gene.phenotypes %}
{{ disease.description }}
{% endfor %}
{% endif %}
{% endmacro %}
{% macro gene_link(gene) %}
{{ gene.hgnc_symbol or gene.hgnc_id }}
{% endmacro %}
{% macro gene_cell(variant, inherit_palette) %}
{% macro panel_badge(variant, gene_id=0) %}
{% set matching_panels = [] %}
{% for panel in variant.case_panels|rejectattr('removed')|list %}
{% if gene_id in panel.hgnc_ids %}
{% set _ = matching_panels.append(panel) %}
{% endif %}
{% endfor %}
{% set panel_count = matching_panels|length %}
{% if panel_count %}
{{ panel_count }}
{% endif %}
{% endmacro %}
{% if variant.category in ["cancer", "sv_cancer"] %}
{% if variant.first_rep_gene %}
{{ gene_link(variant.first_rep_gene) }}
{% endif %}
{% if variant.secondary_gene %}
({{ variant.second_rep_gene.hgnc_symbol or variant.second_rep_gene.hgnc_id }})
{% endif %}
{% if variant.first_rep_gene or variant.second_rep_gene %}
{{ panel_badge(variant, variant.first_rep_gene.hgnc_id or variant.second_rep_gene.hgnc_id) }}
{% endif %}
{% else %}
{% for gene in variant.genes %}
{{ gene_link(gene) }}
{% for model in gene.inheritance %}
{{ inheritance_badge(model, inherit_palette) }}
{% endfor %}
{{ incomplete_penetrance_badge(gene, inherit_palette) }}
{{ panel_badge(variant, gene.hgnc_id) }}
{% endfor %}
{% endif %}
{% 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 or variant.local_obs_cancer_somatic_panel_old %}
Local {% if variant.category in ['snv', 'sv'] %}
{{ variant.local_obs_old or variant.local_obs_cancer_germline_old or variant.local_obs_cancer_somatic_old or variant.local_obs_cancer_somatic_panel_old or 0 }} {% 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() %}
.
{% else %}
{{ allele.alt_freq|round(4) }} {% if 'alt_depth' in allele and allele.alt_depth >= 0 %}{{ allele.alt_depth }}{% else %}.{% endif %}|{% if 'ref_depth' in allele and allele.ref_depth >= 0 %}{{ allele.ref_depth }}{% else %}.{% endif %}
{% else %}
N/A
{% endif %}
{% endmacro %}
{% macro cell_cadd(variant) %}
{% if variant.cadd_score %}
{{ variant.cadd_score|round(1) }}
{% else %}
-
{% endif %}
{% endmacro %}
{% macro overlapping_cell(variant, institute, case) %}
{% if variant.compounds %}
{% set ns=namespace(show_compounds=false) %}
{% for compound in variant.compounds if not compound.is_dismissed %}
{% set ns.show_compounds = true %}
{% endfor %}
{% if ns.show_compounds %}
Compounds
{% endif %}
{% endif %}
{% if variant.overlapping %}
Gene overlapping (DNA)
{% else %}
data-bs-content="Gene overlapping variants in affected individuals
{{ overlapping_tooltip_table(institute, case, variant.overlapping[:40]) }}">Gene overlapping (DNA)
{% endif %}
{% endif %}
{% if variant.overlapping_outliers %}
Gene overlapping (omics)
{% endif %}
{% endmacro %}
{% macro cell_models(variant, genetic_models_palette) %}
{% for model in (variant.genetic_models or []) %}
{% if model in genetic_models_palette %}
{{model}}
{% else %}
{{ model }}
{% endif %}
{% endfor %}
{% if variant.mosaic_tags %}
mosaic
{% endif %}
{% endmacro %}