{% from "cases/utils.html" import variant_transcripts %} {% from "utils.html" import comments_table, variant_related_comments_table %} {% extends "report_base.html" %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} {% endblock %} {% set affected = [] %} {% set printed_vars = [] %} {% block body %}

Scout case analysis report

- created on: {{report_created_at}}

{{ phenotype_panel() }} {{ gene_panels_panel()}} {{ causatives_panel()}} {{ pinned_panel() }} {{ classified_panel() }} {{ tagged_panel() }} {{ commented_panel() }} {{ dismissed_panel() }} [END OF VARIANT REPORT]

{% if coverage_report %}
{{ coverage_report|safe }}

{% endif %} clinical-genomics.github.io/scout
{% endblock %} {% macro phenotype_panel() %}
Case {{ case.display_name }} - Phenotype Overview
{% if case.madeline_info and case.individuals|length > 1 %} {% endif %}
{% if format == 'html' %} {{ case.madeline_info|safe }} {% elif case.madeline_path %} pedigree_img {% endif %}
Case created: {{case.created_at.strftime('%Y-%m-%d')}} Last updated: {{case.updated_at.strftime('%Y-%m-%d') if case.updated_at else "n.a." }}

{% if not cancer %} {% endif %} {% for ind in case.individuals %} {% if not cancer %} {% endif %} {% endfor %}
Sample Sex Status SequencingAncestry (pred.) Parenthood
{{ ind.display_name }} {% if ind.sex == '2' %} F {% elif ind.sex == '1' %} M {% else %} n.a. {% endif %} {% if ind.confirmed_sex %} V {% endif %} {% if ind.phenotype==2 %} {% do affected.append(ind.display_name) %} {{ ind.phenotype_human }} {% else %} {{ ind.phenotype_human }} {% endif %} {{ ind.analysis_type|upper }}{{ ind.predicted_ancestry or 'N/A' }} {% if ind.confirmed_parent == True %} V {% elif ind.confirmed_parent == False %} ! {% else %} N/A {% endif %}
Case status: {% if 'solved' in case.status%} {{case.status.upper()}} {% else %} {{case.status.upper()}} {% endif %}

{% if comments | count_cursor > 0 %} {% else %} {% endif %} {% if audits | count_cursor > 0 %} {% endif %}
{% if case.synopsis %} Synopsis: {{ case.synopsis|markdown }} {% endif %} Associated phenotypes:
{% if case.phenotype_terms %}
    {% for pheno in case.phenotype_terms %}
  • {{pheno.feature}} - ({{pheno.phenotype_id}}) {% for feature_ind in pheno.individuals %} {% for case_ind in case.individuals %} {% if feature_ind.individual_name == case_ind.display_name %} {{case_ind.display_name}} {% endif %} {% endfor %} {% endfor %}
  • {% endfor %}
{% else %} No associated HPO terms. {% endif %}
Associated diagnoses:
{% if case.diagnosis_phenotypes %}
    {% for dia in case.diagnosis_phenotypes %}
  • {{dia.description}} ({{dia.disease_id}}) {% for feature_ind in dia.individuals %} {% for case_ind in case.individuals %} {% if feature_ind.individual_name == case_ind.display_name %} {{case_ind.display_name}} {% endif %} {% endfor %} {% endfor %}
  • {% endfor %}
{% else %} No associated OMIM diagnoses. {% endif %}
Case-related comments
{% for comment in comments %} {% endfor %}
{{comment.created_at.strftime('%Y-%m-%d')}} {{comment.user_name}} {{ comment.content }}
No comments left for this case.
{% set audit_query = namespace() %} {% for audit in audits %} {% set audit_query = audit.link|url_args %} {% endfor %}
Filters marked audited for case
{{ audit.subject }} ({{audit_query.variant_type if audit_query.variant_type else "type unavailable -"}} {{ audit_query.category if audit_query.category else "category unavailable"}}) was marked checked by {{ audit.user_name }} on {{audit.created_at.strftime('%Y-%m-%d')}}.
{% endmacro %} {% macro gene_panels_panel() %}
Default gene panels
{% for panel in case.panels %} {% if panel.is_default %} {% endif %} {% else %} {% endfor %}
Panel Version Genes
{{ panel.display_name|truncate(75, True) }} {{ panel.version }} ({{ panel.updated_at.date() }}) {{ panel.nr_genes }}
No panels linked to case
{% endmacro %} {% macro causatives_panel() %}
Causative Variants
{% if variants.causatives_detailed or variants.partial_causatives_detailed %} {% for causative in variants.causatives_detailed|sort(attribute='variant_rank') + variants.partial_causatives_detailed|sort(attribute='variant_rank') %} {% do printed_vars.append(causative['_id']) %} {{ variant_content(causative, loop.index) }}
{% endfor %} {% else %} No causative variants available for this case {% endif %}
{% endmacro%} {% macro pinned_panel() %}
Pinned Variants
{% set duplicated_variants = [] %} {% if variants.suspects_detailed %} {% if cancer %} {{ somatic_variant_table(variants.suspects_detailed) }} {% endif %} {% for pinned in variants.suspects_detailed|sort(attribute='variant_rank') %} {% if pinned['_id'] not in printed_vars %} {% do printed_vars.append(pinned['_id']) %} {{ variant_content(pinned, loop.index) }} {% else %} {% do duplicated_variants.append(pinned['_id']) %} {% endif %}
{% endfor %} {% else %} No pinned variants available for this case {% endif %} {% if variants.suspects_detailed and duplicated_variants|length == variants.suspects_detailed.suspects_detailed|length %} All pinned variants are described among the causative variants {% endif %}
{% endmacro %} {% macro classified_panel() %}
Other ACMG-classified Variants
{% set duplicated_variants = [] %} {% if variants.classified_detailed %} {% for variant in variants.classified_detailed|sort(attribute='variant_rank') %} {% if variant['_id'] not in printed_vars %} {% do printed_vars.append(variant['_id']) %} {{ variant_content(variant, loop.index) }} {% else %} {% do duplicated_variants.append(variant['_id']) %} {% endif %}
{% endfor %} {% else %} No ACMG-classified variants available for this case {% endif %} {% if variants.classified_detailed and duplicated_variants|length == variants.classified_detailed|length %} All ACMG-classified variants are already described in the previous views {% endif %}
{% endmacro %} {% macro tagged_panel() %}
Other Manual Ranked (Tagged) Variants
{% set duplicated_variants = [] %} {% if variants.tagged_detailed %} {% for variant in variants.tagged_detailed|sort(attribute='variant_rank') %} {% if variant['_id'] not in printed_vars %} {% do printed_vars.append(variant['_id']) %} {{ variant_content(variant, loop.index) }} {% else %} {% do duplicated_variants.append(variant['_id']) %} {% endif %}
{% endfor %} {% endif %} {% if variants.tier_detailed %} {% for variant in variants.tier_detailed|sort(attribute='variant_rank') %} {% if variant['_id'] not in printed_vars %} {% do printed_vars.append(variant['_id']) %} {{ variant_content(variant, loop.index) }} {% else %} {% do duplicated_variants.append(variant['_id']) %} {% endif %}
{% endfor %} {% endif %} {% if not (variants.tagged_detailed or variants.tier_detailed) %} No tagged variants for this case {% endif %} {% if (variants.tagged_detailed or variants.tier_detailed) and duplicated_variants|length == (variants.tagged_detailed|length+variants.tier_detailed|length) %} All tagged variants are already described in the previous views {% endif %}
{% endmacro %} {% macro variant_content(variant, index) %} {% if variant.category == 'snv' %} {{ sn_variant_content(variant, index) }} {% elif variant.category == 'cancer' %} {{ sn_variant_content(variant, index) }} {% elif variant.category == 'str' %} {{ str_variant_content(variant, index) }} {% else %} {{ sv_variant_content(variant, index) }} {% endif %} {% endmacro %} {% macro commented_panel() %}
Other Commented Variants
{% set duplicated_variants = [] %} {% if variants.commented_detailed %} {% for variant in variants.commented_detailed|sort(attribute='variant_rank') %} {% if variant['_id'] not in printed_vars %} {% do printed_vars.append(variant['_id']) %} {% if variant.category == 'snv' %} {{ sn_variant_content(variant, loop.index) }} {% elif variant.category == 'cancer' %} {{ sn_variant_content(variant, loop.index) }} {% elif variant.category == 'str' %} {{ str_variant_content(variant, loop.index) }} {% else %} {{ sv_variant_content(variant, loop.index) }} {% endif %} {% else %} {% do duplicated_variants.append(variant['_id']) %} {% endif %}
{% endfor %} {% else %} No commented variants for this case {% endif %} {% if variants.commented_detailed and duplicated_variants|length == variants.commented_detailed|length %} All commented variants are already described in the previous views {% endif %}
{% endmacro %} {% macro sn_variant_content(variant, index) %}
# {{variant.display_name[:30]}}  {{variant.category | upper}}  {% if variant.sanger_ordered and variant.validation %} Verification:{{variant.validation}} {% elif variant.sanger_ordered %} Verification ordered {% endif %}
{{ variant_phenotypes(variant) }}
{% if variant.cytoband_start and variant.cytoband_end %} {% else %} {% endif %}
Coordinates Cytoband nucl. change SNP ids Gene panels
chr{{variant.chromosome}}:{{variant.position}}-{{variant.end}}{{variant.cytoband_start}}-{{variant.cytoband_end}}-{{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 %} {% if variant.panels%} {% if variant.panels|length <= 3 %} {% for panel_id in variant.panels %} {{ panel_id }}
{% endfor %} {% else %} {{ variant.panels|length }} panels {% endif %} {% endif %}
{{ genotype_table(variant) }}
Pop. frequency {% if variant.frequency == 'common' %} {{variant.frequency}} {% elif variant.frequency == 'uncommon' %} {{variant.frequency}} {% else %} {{variant.frequency}} {% endif %}
{% if variant.dbsnp_id %} 1000G {% else %} 1000G {% endif %} {% if variant.max_thousand_genomes_frequency %} {{ variant.max_thousand_genomes_frequency|human_decimal }} (max) | {% endif %} {{ variant.thousand_genomes_frequency|human_decimal if variant.thousand_genomes_frequency }} {% if not variant.max_thousand_genomes_frequency and not variant.thousand_genomes_frequency %} Not annotated {% endif %}
ExAC {% if variant.max_exac_frequency %} {{ variant.max_exac_frequency|human_decimal }} (max) | {% endif %} {{ variant.exac_frequency|human_decimal if variant.exac_frequency }} {% if not variant.max_exac_frequency and not variant.exac_frequency %} Not annotated {% endif %}
gnomAD {% if 'gnomad_frequency' in variant%} {% if variant.max_gnomad_frequency %} {{ variant.max_gnomad_frequency|human_decimal }} (max) | {% endif %} {{ variant.gnomad_frequency|human_decimal if variant.gnomad_frequency }} {% else %} Not annotated {% endif %}
{% if not cancer %} {% endif %} {% if not cancer %} {% endif %}
Scout Rank Scout score Manual rank CADD scoreInheritance modelsACMG classification
{{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 variant.genetic_models %} {% for model in variant.genetic_models|sort %} {{ model }} {% endfor %} {% else %} No models followed {% endif %} {% if variant.acmg_classification %} {{variant.acmg_classification['code'] }} {% else %} - {% endif %}
{% if variant.genes %} {% for gene in variant.genes %} {% endfor %} {% endif %}
Affected gene(s) Description Region annotation Transcript - HGVS - Protein OMIM phenotypes [inheritance]
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {{gene.description|title}} {{gene.region_annotation}} {{ variant_transcripts(gene) }}
    {% for disease_term in gene.disease_terms %}
  • {{ disease_term.description }} {{ disease_term.inheritance }}
  • {% endfor %}
{% if variant.comments | count_cursor > 0 %} {{ variant_related_comments_table(variant, case) }} {% endif %}
{% endmacro %} {% macro dismissed_gene_list(variant) %} {% if variant.genes %} {% if variant.genes|length > 3%} {{ variant.hgnc_symbols|length }} genes {% else %} {% for gene in variant.genes %} {{ gene.hgnc_symbol }} {{gene.region_annotation}}
{% endfor %} {% endif %} {% else %} - {% endif %} {% endmacro %} {% macro dismissed_panel() %}

Dismissed Variants

{% if variants.dismissed_detailed %} {% for variant in variants.dismissed_detailed|sort(attribute='variant_rank') %} {% endfor %}
Variant Category Genes Dismissed description
#{{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}} {{ dismissed_gene_list(variant) }}
    {% for reason in variant.dismiss_variant if not reason == "Select a tag" %}
  • {{dismissed_options[reason|int]['description']}} {% if reason == '2' and variant.category == 'snv'%}
    Pop. frequency {% if variant.frequency == 'common' %} {{variant.frequency}} {% elif variant.frequency == 'uncommon' %} {{variant.frequency}} {% else %} {{variant.frequency}} {% endif %}
    {% if variant.dbsnp_id %} 1000G {% else %} 1000G {% endif %} {% if variant.max_thousand_genomes_frequency %} {{ variant.max_thousand_genomes_frequency|human_decimal }} (max) | {% endif %} {{ variant.thousand_genomes_frequency|human_decimal if variant.thousand_genomes_frequency }} {% if not variant.max_thousand_genomes_frequency and not variant.thousand_genomes_frequency %} Not annotated {% endif %}
    ExAC {% if variant.max_exac_frequency %} {{ variant.max_exac_frequency|human_decimal }} (max) | {% endif %} {{ variant.exac_frequency|human_decimal if variant.exac_frequency }} {% if not variant.max_exac_frequency and not variant.exac_frequency %} Not annotated {% endif %}
    gnomAD {% if 'gnomad_frequency' in variant%} {% if variant.max_gnomad_frequency %} {{ variant.max_gnomad_frequency|human_decimal }} (max) | {% endif %} {{ variant.gnomad_frequency|human_decimal if variant.gnomad_frequency }} {% else %} Not annotated {% endif %}
    {% elif reason == '7' %}
    ({% if variant.genetic_models %} {% for model in variant.genetic_models|sort %} {{model}} {% endfor %} {% else %} No models followed {% endif %})
    {% elif reason== '23' %} {% for sample in variant.samples %} {% if sample.allele_depths %} {% for number in sample.allele_depths %} {% endfor %} {% else %} {% endif %} {% endfor %}
    Sample Genotype (GT) Allele depth (AD) Genotype quality
    Ref. Alt.
    {{ sample.display_name }} {{ sample.genotype_call }}{{ number }}N/A N/A{{ sample.genotype_quality }}
    {% endif %}
  • {% endfor %}
{% if variant.comments | count_cursor > 0 %} {{ comments_table(institute, case, variant.comments) }} {% endif %}
{% else %} No dismissed variants for this case {% endif %}
{% endmacro %} {% macro sv_variant_content(variant,index) %}
{{ variant_phenotypes(variant) }}
{% if variant.cytoband_start and variant.cytoband_end %} {% else %} {% endif %}
Variant type length Coordinates Cytoband Gene panels Callers
{{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 %} {{variant.cytoband_start}}-{{variant.cytoband_end}}- {% if variant.panels %} {% if variant.panels|length <= 3 %} {% for panel_id in variant.panels %} {{ panel_id }}
{% endfor %} {% else %} {{ variant.panels|length }} panels {% endif %} {% endif %}
{% if variant.callers %} {% for caller,call in variant.callers|sort %} {{ caller+':'+call }} {% endfor %} {% else %} - {% endif %}
{{genotype_table(variant)}} {% for freq_name, value, link in variant.frequencies %} {% endfor %}
Pop. frequency
{{ freq_name }} {% if value %} {{ value|human_decimal }} {% else %} Not annotated {% endif %}
{% if not cancer %} {% endif %}
Scout Rank Scout score Manual rankInheritance modelsACMG classification
{{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 %} {% if variant.genetic_models %} {% for model in variant.genetic_models|sort %} {{ model }} {% endfor %} {% else %} No models followed {% endif %} {% if variant.acmg_classification %} {{variant.acmg_classification['code'] }} {% else %} - {% endif %}
{% if variant.genes and variant.genes|length <= 3 %} {% for gene in variant.genes %} {% endfor %} {% elif variant.genes %} {% endif %}
Affected gene(s) Description Region annotation Transcript - HGVS - Protein OMIM phenotypes [inheritance]
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {{gene.description|title}} {{gene.region_annotation}} {{ variant_transcripts(gene) }}
    {% for disease_term in gene.disease_terms %}
  • {{ disease_term.description }} {{ disease_term.inheritance }}
  • {% endfor %}
{{ 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 %}
{% if variant.comments | count_cursor > 0 %}
{{ variant_related_comments_table(variant, case) }} {% endif %}
{% endmacro %} {% macro str_variant_content(variant,index) %}
{{ variant_phenotypes(variant) }}
{% if not variant.str_status or variant.str_status == 'normal' %} {% elif variant.str_status == 'full_mutation' %} {% elif variant.str_status == 'pre_mutation' %} {% endif %}
Variant type Estimated size Reference size Coordinates Gene panels
{{variant.category | upper}} {{ variant.alternative|replace("STR", "")|replace("<", "")|replace(">", "") }} {{ 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 %} {% if variant.panels %} {% if variant.panels|length <= 3 %} {% for panel_id in variant.panels %} {{ panel_id }}
{% endfor %} {% else %} {{ variant.panels|length }} panels {% endif %} {% endif %}
{% for sample in variant.samples %} {% if sample.allele_depths %} {% for number in sample.allele_depths %} {% endfor %} {% else %} {% endif %} {% endfor %}
Sample Genotype (GT) Allele depth (AD) ExpansionHunter support
Reference Alternative
{{ sample.display_name }} {{ sample.genotype_call }} {% if number == -1 %} N/A {% else %} {{ number }} {% endif %} N/A N/A{{ sample.so }}
Scout Rank Scout score Manual rank
{{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 %}
{% if variant.str_disease %} {% else %} {% endif %}
Disease Inheritance model Source
{{ variant.str_disease }}- {{ variant.str_inheritance_mode if variant.str_inheritance_mode else "-" }} {% if variant.str_source.display %} {{ variant.str_source.display }} {% else %} "-" {% endif %}
{% if variant.comments | count_cursor > 0 %}
{{ variant_related_comments_table(variant, case) }} {% endif %}
{% endmacro %} {% macro variant_phenotypes(variant) %} {% if variant.get('phenotypes') %}
Partial causative OMIM terms: {{ variant['phenotypes'].get('diagnosis_phenotypes')|join(' ')}} - HPO terms:  {%- for hpo_term in variant['phenotypes'].get('phenotype_terms') -%} {{ hpo_term.phenotype_id}}({{hpo_term.feature}})  {%- endfor -%}
{% endif %} {% endmacro %} {% macro genotype_table(variant) %} {% if cancer %} {% else %} {% endif %} {% for sample in variant.samples %} {% if sample.allele_depths %} {% for number in sample.allele_depths %} {% endfor %} {% else %} {% endif %} {% if cancer %} {% if sample.read_depth and sample.allele_depths[1] != -1 %} {% else %} {% endif %} {% else %} {% endif %} {% endfor %}
Sample Genotype (GT) Allele depth (AD)VAFGenotype quality (GQ)
Reference Alternative
{{ sample.display_name }} {{ sample.genotype_call }}{{ number }}N/A N/A{{ (sample.allele_depths[1]/sample.read_depth)|round(4) }}N/A{{ sample.genotype_quality }}
{% endmacro %} {% macro somatic_variant_table(variants) %}
Summary table
{% for acmg in ["P","LP", "VUS", "LB", "B", ] %} {% for variant in variants|selectattr("acmg_classification", "defined")|selectattr("acmg_classification.short", "equalto", acmg)|selectattr("first_rep_gene.hgnc_symbol", "defined")|sort(attribute='first_rep_gene.hgnc_symbol') %} {{ variant_table_line(variant) }} {% endfor %} {% endfor %} {% for variant in variants|selectattr("acmg_classification", "defined")|selectattr("acmg_classification.short", "undefined")|selectattr("first_rep_gene.hgnc_symbol", "defined")|sort(attribute='first_rep_gene.hgnc_symbol') %} {{ variant_table_line(variant) }} {% endfor %} {% for variant in variants|selectattr("acmg_classification", "undefined")|selectattr("first_rep_gene.hgnc_symbol", "defined")|sort(attribute='first_rep_gene.hgnc_symbol') %} {{ variant_table_line(variant) }} {% endfor %} {% for variant in variants|selectattr("first_rep_gene.hgnc_symbol", "undefined") %} {{ alt_variant_line(variant) }} {% endfor %}
Gene Symbol Transcript HGVS c. HGVS p. Tumor VAF% ACMG
{% endmacro %} {% macro variant_table_line(variant) %} {{ variant.first_rep_gene.hgnc_symbol or variant.first_rep_gene.hgnc_id }} {% if variant.sub_category != "snv" %}{{ variant.sub_category|upper }}{% endif %} {{ variant.first_rep_gene.canonical_transcript }} {{ (variant.first_rep_gene.hgvs_identifier or variant.display_name)|truncate(20, True) }} {{ (variant.first_rep_gene.hgvsp_identifier or '') |url_decode|truncate(30, True) }} {% for sample in variant.samples %}{% if sample.is_affected %} {{ (sample.allele_depths[1]/sample.read_depth*100)|round|int }}{% endif %} {% endfor %} {% if variant.acmg_classification %} {{variant.acmg_classification['short'] }} {% elif variant.manual_rank %} {{ manual_rank_options[variant.manual_rank]['label'] }} {% else %} - {% endif %} {% endmacro %} {% macro alt_variant_line(variant) %} chr {{ variant.chromosome }} {{ variant.sub_category|upper }} pos {{ variant.position }} {% if variant.category in ['cancer_sv', 'sv'] %} chr {{ variant.end_chrom }} {% else %} {{ variant.reference|truncate(20, True) }} {% endif %} {% if variant.category in ['cancer_sv', 'sv'] %} end {{ variant.end }} {% else %} {{ variant.alternative|truncate(20, True) }} {% endif %} {% for sample in variant.samples %}{% if sample.is_affected %} {{ (sample.allele_depths[1]/sample.read_depth*100)|round|int }}{% endif %} {% endfor %} {% if variant.acmg_classification %} {{variant.acmg_classification['short'] }} {% elif variant.manual_rank %} {{ manual_rank_options[variant.manual_rank]['label'] }} {% else %} - {% endif %} {% endmacro %}