{% extends "report_base.html" %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} {% endblock %} {% set affected = [] %} {% set printed_vars = [] %} {% block body %}
{% if case.madeline_info and case.individuals|length > 1 %}
{% if format == 'html' %}
{{ case.madeline_info|safe }}
{% else %}
{% endif %}
{% else %}
Single sample family. No pedigree available. {% endif %} |
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Case status:
{% if 'solved' in case.status%}
{{case.status.upper()}}
{% else %}
{{case.status.upper()}}
{% endif %}
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{% if case.synopsis %} Synopsis: {{ case.synopsis|markdown }} {% endif %} |
Associated phenotypes: {% if case.phenotype_terms %}
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Panel | Version | Genes | ||
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{{ panel.display_name|truncate(75, True) }} | {{ panel.version }} ({{ panel.updated_at.date() }}) | {{ panel.nr_genes }} | ||
No panels linked to case |
Coordinates | Cytoband | nucl. change | dbsnp id | Gene panels | |
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chr{{variant.chromosome}}:{{variant.position}}-{{variant.end}} | {% if variant.cytoband_start and variant.cytoband_end %}{{variant.cytoband_start}}-{{variant.cytoband_end}} | {% else %}- | {% endif %}{{variant.reference}} → {{variant.alternative}} | {% if variant.dbsnp_id %} {{variant.dbsnp_id}} {% else %} - {% endif %} | {% for panel_id in variant.panels %} {{ panel_id }} {% endfor %} |
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Scout Rank | Scout score | Manual rank | CADD score | Inheritance models | ACMG classification |
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{{variant.variant_rank}} | {{variant.rank_score}} | {% if variant.manual_rank %} {{ manual_rank_options[variant.manual_rank]['label'] }} {% endif %} {% if variant.cancer_tier %} {{ cancer_tier_options[variant.cancer_tier]['label'] }} {% endif %} {% if not (variant.manual_rank or variant.cancer_tier) %} - {% endif %} | {{ variant.cadd_score or '-' }} | {% for model in variant.genetic_models|sort %} {{ model }} {% else %} No models followed {% endfor %} | {% if variant.acmg_classification %} {{variant.acmg_classification['code'] }} {% else %} - {% endif %} |
Affected gene(s) | Description | Region annotation | Transcript - HGVS - Protein | OMIM phenotypes [inheritance] |
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{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} | {{gene.description|title}} | {{gene.region_annotation}} |
{% set n_primary_transcripts = [] %}
{% set hgnc_prim = namespace(primary=None) %}
{% endif %} |
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Variant-related comments | |||
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Variant name | Genes | Dismissed description | ||||||||||||||||||||||||
#{{loop.index}} | {% if variant.category == 'snv' %}{{variant.display_name[:30]}} | {% else %}chr{{variant.chromosome}}:{{variant.position}}_{{variant.sub_category|upper}} | {% endif %}
{% for gene in variant.genes %}
{{ gene.hgnc_symbol }} {{gene.region_annotation}} {% endfor %} |
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Variant type | length | Coordinates | Cytoband | Gene panels | Callers | |
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{{variant.sub_category|upper}} | {{ variant.length }} | {% if variant.chromosome == variant.end_chrom %} chr{{variant.chromosome}}:{{variant.position}}-{{variant.end}} {% else %} chr{{variant.chromosome}}:{{variant.position}}/{{'chr'+variant.end_chrom}}:{{variant.end}} {% endif %} | {% if variant.cytoband_start and variant.cytoband_end %}{{variant.cytoband_start}}-{{variant.cytoband_end}} | {% else %}- | {% endif %}
{% for panel_id in variant.panels %}
{{ panel_id }} {% endfor %} |
{% if variant.callers %} {% for caller,call in variant.callers|sort %} {{ caller+':'+call }} {% endfor %} {% else %} - {% endif %} |
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Scout Rank | Scout score | Manual rank | Inheritance models | ACMG classification |
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{{variant.variant_rank}} | {{variant.rank_score}} | {% if variant.manual_rank %} {{ manual_rank_options[variant.manual_rank]['label'] }} {% endif %} {% if variant.cancer_tier %} {{ cancer_rank_options[variant.cancer_tier]['label'] }} {% endif %} {% if not (variant.manual_rank or variant.cancer_tier) %} - {% endif %} | {% for model in variant.genetic_models|sort %} {{ model }} {% else %} No models followed {% endfor %} | {% if variant.acmg_classification %} {{variant.acmg_classification['code'] }} {% else %} - {% endif %} |
Affected gene(s) | Description | Region annotation | Transcript - HGVS - Protein | OMIM phenotypes [inheritance] |
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{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} | {{gene.description|title}} | {{gene.region_annotation}} |
{% set n_primary_transcripts = [] %}
{% endif %} |
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Variant-related comments | ||
{{comment.created_at.strftime('%Y-%m-%d')}} | {{comment.user_name}}: | {{ comment.content }} |