{% from "cases/utils.html" import variant_transcripts, filter_audits %} {% from "utils.html" import comments_table, variant_related_comments_table %} {% from "variant/gene_disease_relations.html" import inheritance_badge %} {% from "variants/components.html" import fusion_variants_header, default_fusion_variant_cells %} {% from "variant/variant_details.html" import frequencies_table, old_observations_table %} {% from "variant/components.html" import clinsig_table %} {% extends "report_base.html" %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} {% endblock %} {% set affected = [] %} {% set printed_vars = [] %} {% block body %}
{% if format == 'html' %}
{{ case.madeline_info|safe }}
{% elif case.madeline_path %}
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{% 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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{{filter_audits(audits)}} |
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 | SNP ids | 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 %} {% set dbsnp_ids = variant.dbsnp_id.split(';') %} {% for snp in dbsnp_ids %} {% if "rs" in snp %} dbSNP:{{ snp }} {% else %} ClinVar:{{ snp }} {% endif %} {% endfor %} {% else %} - {% endif %} | {{ overlapping_panels(variant) }} |
{{ genotype_table(variant) }} {{ clinsig_table(variant) }} |
{{ frequencies_table(variant) }} {{ old_observations_table(variant) }} |
Rank | Score | Manual rank | CADD score | {% if not cancer %}Inheritance models | {% endif %}ACMG classification | Bayesian classification | {% if cancer %}ClinGen-CGC-VICC classification | {% endif %}
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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 %} | {% if variant.cadd_score %} {{ variant.cadd_score|round(1) }} {% else %} - {% endif %} | {% if not cancer %}{% if variant.genetic_models %} {% for model in variant.genetic_models|sort %} {{ model }} {% endfor %} {% else %} No models followed {% endif %} | {% endif %}{% if variant.acmg_classification %} {{variant.acmg_classification['label'] }} {% else %} - {% endif %} | {% if variant.bayesian_acmg %} Score {{variant.bayesian_acmg.points|string}} {{variant.bayesian_acmg.temperature}} ({{variant.bayesian_acmg.point_classification}}) {% else %} - {% endif %} | {% if cancer %}{% if variant.ccv_classification %} {{variant.ccv_classification['label'] }} {% else %} - {% endif %} {% if variant.bayesian_ccv %} Score {{variant.bayesian_ccv.points|string}} {% if variant.bayesian_ccv.point_classification == "VUS" %} {{variant.bayesian_ccv.temperature}} {% endif %} {% endif %} | {% endif %}
SIFT | REVEL score | REVEL rank score | Polyphen | SPIDEX | SpliceAI DS max |
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{{ variant.sift_predictions|join(', ') or '-'}} | {% if variant.revel %} {{ variant.revel }} {% else %} – {% endif %} | {{ variant.revel_score or '-' }} | {{ variant.polyphen_predictions|join(', ') or '-' }} | {{ variant.spidex|spidex_human if variant.spidex else none|spidex_human }} | {% set spliceai_highest = variant.spliceai_scores | spliceai_max %} {% if spliceai_highest %} {{ variant.spliceai_scores|join(', ') }} {% else %} – {% endif %} |
Affected gene(s) | Description | Region annotation | Consequence | Transcript - HGVS - Protein | Diagnoses [inheritance] |
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{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} | {{gene.description|title}} | {{gene.region_annotation}} | {{gene.functional_annotation.replace("_"," ")|truncate(20, True)}} | {{ variant_transcripts(gene) }} |
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Variant | Category | Genes | Classification | Dismissed description | |||||||||||||||||||||||
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#{{loop.index}} | {% if variant.category == 'snv' %} {{variant.display_name[:30]}} {% elif variant.category == 'cancer' %} {{variant.display_name[:30]}} {% elif variant.category == 'sv' %} chr{{variant.chromosome}}:{{variant.position}}_{{variant.sub_category|upper}} {% else %} rep. {{variant.str_repid}} {% endif %} | {{variant.category|upper}} | {% if variant.acmg_classification %} {{variant.acmg_classification['short'] }} {% endif %} {% if variant.ccv_classification %} {{variant.ccv_classification['short'] }} {% endif %} |
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{% if variant.comments | count_cursor > 0 %} {{ comments_table(institute, case, variant.comments) }} {% endif %} |
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 or variant.chromosome}}:{{variant.end}} {% endif %} | {% if variant.cytoband_start and variant.cytoband_end %}{{variant.cytoband_start}}-{{variant.cytoband_end}} | {% else %}- | {% endif %}{{ overlapping_panels(variant) }} | {% if variant.callers %} {% for caller,call in variant.callers|sort %} {{ caller+':'+call }} {% endfor %} {% else %} - {% endif %} |
{{genotype_table(variant)}} | {{ frequencies_table(variant) }} {{ old_observations_table(variant) }} |
{{variant.variant_rank}} | {% if variant.cancer_tier %} {{ cancer_tier_options[variant.cancer_tier]['label'] }} {% endif %} {% if variant.acmg_classification %} {{variant.acmg_classification['code'] }} {% endif %} | {{ default_fusion_variant_cells(institute, case, variant) }}
Rank | Score | Manual rank | {% if not cancer %}Inheritance models | {% endif %}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 %} | {% if not cancer %}{% if variant.genetic_models %} {% for model in variant.genetic_models|sort %} {{ model }} {% endfor %} {% else %} No models followed {% endif %} | {% endif %}{% if variant.acmg_classification %} {{variant.acmg_classification['code'] }} {% else %} - {% endif %} |
Affected gene(s) | Description | Region annotation | Transcript - HGVS - Protein | Diagnoses [inheritance] |
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{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} | {{gene.description|title}} | {{gene.region_annotation}} | {{ variant_transcripts(gene) }} |
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{{ variant.hgnc_symbols|length }} affected gene(s) | {% if variant.hgnc_symbols|length() <= 10 %} {{ variant.hgnc_symbols|sort|join(" ") }} {% elif genes_in_panels %} Genes matching one or more case default gene panels: {{ variant.hgnc_symbols|list_intersect(genes_in_panels)|sort|join(" ") }} {% endif %} | {% endif %}
Variant type | Estimated size | Reference size | Coordinates | Gene panels |
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{{variant.category | upper}} | {{ variant.str_mc }} | {{ variant.str_ref }} | {% if variant.chromosome == variant.end_chrom %} chr{{variant.chromosome}}:{{variant.position}}-{{variant.end}} {% else %} chr{{variant.chromosome}}:{{variant.position}}/chr{{variant.end_chrom or variant.chromosome}}:{{variant.end}} {% endif %} | {{ overlapping_panels(variant) }} |
Sample | Genotype (GT) | Allele depth (AD) | ExpansionHunter support | ||
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Reference | Alternative | ||||
{{ sample.display_name }} | {{ sample.genotype_call }} | {% if sample.allele_depths %} {% for number in sample.allele_depths %}{% if number == -1 %} N/A {% else %} {{ number }} {% endif %} | {% endfor %} {% else %}N/A | N/A | {% endif %}{{ sample.so }} |
Rank | Score | Manual rank |
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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 %} |
Disease | Inheritance model | Source | |
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{{ variant.str_disease }} | {% else %}- | {% endif %}{{ variant.str_inheritance_mode if variant.str_inheritance_mode else "-" }} | {% if variant.str_source and variant.str_source.display %} {{ variant.str_source.display }} {% else %} "-" {% endif %} |
Sample | Genotype (GT) | Allele depth (AD) | {% if cancer %}VAF | {% else %}Genotype quality (GQ) | {% endif %}|||
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Reference | Alternative | ||||||
{{ sample.display_name }} | {{ sample.genotype_call }} | {% if sample.allele_depths %} {% for number in sample.allele_depths %}{{ number }} | {% endfor %} {% else %}N/A | N/A | {% endif %} {% if cancer %} {% if sample.read_depth and sample.allele_depths[1] != -1 %}{{ (sample.allele_depths[1]/sample.read_depth)|round(4) }} | {% else %}N/A | {% endif %} {% else %}{{ sample.genotype_quality }} | {% endif %}
Gene Symbol | Transcript | HGVS c. | HGVS p. | Tumor VAF% | ACMG |
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