{% extends "layout_bs4.html" %} {% from "utils.html" import comments_panel, activity_panel, pedigree_panel %} {% from "variants/utils.html" import compounds_table, modal_causative %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }} {% endblock %} {% block css %} {{ super() }} {% endblock %} {% block top_nav %} {{ super() }} {% endblock %} {% block top_nav_right %} {% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {% endif %} {{ super() }} {% endblock %} {% block content_main %}
{% if variant.missing_data %}
Showing only first 30 genes!
{% endif %}
{{ matching_variants() }}
{{ panel_basics() }}
{{ panel_summary() }}
{{ transcript_overview() }}
{{ inheritance_panel() }}
{{ omim_phenotypes() }}
{{ frequency_list() }}
{{ severity_list() }}
{{ comments_panel(institute, case, current_user, variant.comments, variant_id=variant._id) }}
{{ gtcall_panel() }}
{% set has_pedigree = case.madeline_info and case.individuals|length > 1 %} {% if has_pedigree %}
{{ pedigree_panel(case) }}
{% endif %}
{% if variant.compounds %}
{{ compounds_panel() }}
{% endif %}
{{ rankscore_panel() }}
{{ overlapping_panel() }}
{{ external_links() }}
{{ activity_panel(events|reverse) }}
{% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {{ modal_sanger() }} {% endif %} {% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {{ modal_cancel_sanger() }} {% endif %}
{{ modal_causative(case, institute, variant) }} {% endblock %} {% macro sanger_button() %} {% if variant.sanger_ordered %} {% if variant.validation in ['True positive', 'False positive']%} {% else %} {% endif %} {% else %} {% endif %} {% endmacro %} {% macro sanger_form() %} {% endmacro %} {% macro pin_button() %} {% if variant._id not in case.suspects %}
{% else %}
{% endif %} {% endmacro %} {% macro causative_button() %} {% if variant._id in case.causatives %}
{% elif variant._id in case.partial_causatives %}
{% else %} {% endif %} {% endmacro %} {% macro matching_variants() %}
{% if causatives %}
Matching causatives from other cases
{% else %}
No matching causative variants
{% endif%}
{% endmacro %} {% macro panel_basics() %}
Basics
Position {{ variant.chromosome }}:{{ variant.position }} {% if variant.is_par %} PAR {% endif %} Change {{ variant.reference }} → {{ variant.alternative }}
{% for gene in variant.genes %} {% endfor %}
Gene Region Function
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {{ gene.region_annotation }} {{ gene.functional_annotation|truncate(20, True) }}
{{ acmg_form(variant.acmg_classification.code if variant.acmg_classification) }}
Classify {% if variant._id in case.suspects and not variant.clinvar_clinsig %} Submit to ClinVar {% endif %} {% if variant.clinvar_clinsig %} Modify clinvar submission {% endif %}
{% if evaluations %}
{% for evaluation in evaluations %} {{ acmg_classification_item(evaluation) }} {% endfor %}
{% endif %}
{% endmacro %} {% macro panel_summary() %}
Summary
Rank {{ variant.variant_rank }} Rank score {{ variant.rank_score }} CADD score {{ variant.cadd_score or '-' }}
Matches OMIM inhert. {% if variant.is_matching_inheritance %} Yes {% else %}
No
{% endif %}
Frequency
{{ variant.frequency }}
{% if variant.clinsig_human %} {% for clinsig in variant.clinsig_human %} {% else %} No annotations {% endfor %}
CLINSIG Accession Revstat
{{ clinsig.human }} {{ clinsig.accession }} {{ clinsig.revstat }}
{% endif %}
Gene coverage
{% if config.SQLALCHEMY_DATABASE_URI %} {% for gene in variant.genes %} {% endfor %} {% endif %}
{% if variant.chromosome == "MT" %} {% if case.mt_bams %} IGV viewer {% else %} MT BAM file(s) missing {% endif %} {% elif case.bam_files %} IGV viewer {% else %} BAM file(s) missing {% endif %} {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
{% endmacro %} {% macro transcript_overview() %}
Disease associated transcripts
{{ variant.disease_associated_transcripts|join(', ') if variant.disease_associated_transcripts else '-' }}
Transcript overview
{% for gene in variant.genes %} {% if not variant.has_refseq %} {% for transcript in gene.transcripts %} {% endfor %} {% else %} {% for transcript in gene.primary_transcripts %} {% for refseq_id in transcript.refseq_identifiers %} {% endfor %} {% endfor %} {% endif %} {% endfor %}
Gene Transcript HGVS Description
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {% if transcript.is_canonical %} C {% endif %}
{{ transcript.transcript_id }}
{{ (transcript.coding_sequence_name or '')|truncate(20, True) }} {{ (transcript.protein_sequence_name or '')|url_decode }}
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {% if transcript.is_canonical %} C {% endif %}
{{ refseq_id }} ({{ transcript.transcript_id }}) {% if refseq_id in gene.common.primary_transcripts %} (hgnc-primary) {% endif %}
{{ (transcript.coding_sequence_name or '')|truncate(20, True) }} {{ (transcript.protein_sequence_name or '')|url_decode }}
{% endmacro %} {% macro frequency_list() %}
Frequency
{% if config.LOQUSDB_SETTINGS %}
Local observations
Local observations (archive 2017-05-31)
{% endif %}
{% endmacro %} {% macro severity_list() %}
Severity
Conservation
Mappability (fracMatch)
{% set superdups_fracmatches = [] %} {% for gene in variant.genes %} {% for transcript in gene.transcripts %} {% if transcript.superdups_fracmatch %} {% for superdup in transcript.superdups_fracmatch %} {% do superdups_fracmatches.append(superdup) %} {% endfor %} {% endif %} {% endfor %} {% endfor %} {% set superdups_fracmatches = superdups_fracmatches|sort %}
{% if superdups_fracmatches %} mapping to {{superdups_fracmatches|length}} segm. dups. (min matching:{{ superdups_fracmatches|first|float|round(3) }}, max matching:{{ superdups_fracmatches|last|float|round(3) }}) {% else %} - {% endif %}
{% endmacro %} {% macro inheritance_panel() %}
Gene annotations
{% if variant.azlength %}
Autozygous region
Length {{ variant.azlength }} Qual {{ variant.azqual }}
{% endif %}
Gene models:
{% for gene in variant.genes %} {% endfor %}
Gene Inheritance Penetrance
OMIM Manual OMIM Manual
{{ gene.hgnc_symbol }} {% for model in gene.omim_inheritance %} {{ model }} {% endfor %} {% for model in gene.manual_inheritance %} {{ model }} {% endfor %} {% if gene.omim_penetrance %} yes {% else %} no {% endif %} {% if gene.manual_penetrance %} yes {% else %} no {% endif %}
{% endmacro %} {% macro omim_phenotypes() %}
OMIM
{% for gene in variant.genes %} {% for disease_term in gene.disease_terms %} {% else %} {% if gene.common %} {% endif %} {% endfor %} {% endfor %}
Gene Phenotype Inheritance model
{% if gene.common %} {{ gene.common.hgnc_symbol }} {% else %} {{ gene.hgnc_id }} {% endif %} {{ disease_term.description }} {{ disease_term.inheritance|join(', ') }}
{{ gene.common.hgnc_symbol }}
{% endmacro %} {% macro gtcall_panel() %}
GT call {% if variant.is_par %} PAR {% 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) Genotype quality (GQ)
Reference Alternative
{{ sample.display_name }} {{ sample.genotype_call }}{{ number }}N/A N/A{{ sample.genotype_quality }}
{% endmacro %} {% macro compounds_panel() %}
Compounds (top 20)
{{ compounds_table(institute, case, variant.compounds[:20]) }}
{% endmacro %} {% macro rankscore_panel() %}
Rank score results
{% for result in variant.rank_score_results %} {% endfor %} {% for result in variant.rank_score_results %} {% endfor %}
{{ result.category|replace('_', ' ') }}
{{ result.score }}
{% endmacro %} {% macro overlapping_panel() %}
Overlapping SVs
{% for sv_variant in overlapping_svs %} {% else %} {% endfor %}
Variant Gene Type Combined score Rank score Length Region Function
{{ sv_variant.display_name|truncate(20, True) }} {{ sv_variant.hgnc_symbols|join(', ')|truncate(40, True) }} {{ sv_variant.sub_category|upper }} {{ variant.rank_score + sv_variant.rank_score }} {{ sv_variant.rank_score }} {{ sv_variant.length }} {{ sv_variant.region_annotations|join(', ')|truncate(40, True) }} {{ sv_variant.functional_annotations|join(', ')|truncate(40, True) }}
No overlapping SVs found
{% endmacro %} {% macro genes_panel() %}
{% for gene in variant.genes %} {% endfor %}
Gene Ensembl ID Description
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {% if gene.common %} {{ gene.common.ensembl_id }} {% endif %} {{ gene.common.description if gene.common }}
{% endmacro %} {% macro transcripts_panel() %}
{% for gene in variant.genes %} {% for transcript in gene.transcripts %} {% endfor %} {% endfor %}
Gene Transcript RefSeq Biotype Mutation type Strand Exon Intron cDNA Amino acid
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {{ transcript.transcript_id }} {% if transcript.is_canonical %} C {% endif %} {{ transcript.refseq_identifiers|join(',') }} {{ transcript.biotype or '' }} {{ transcript.functional_annotations |join(', ') |truncate(20, True) }} {{ transcript.strand }} {{ transcript.exon or '' }} {{ transcript.intron or '' }} {{ (transcript.coding_sequence_name or '') }} {{ (transcript.protein_sequence_name or '')|url_decode }}
{% endmacro %} {% macro proteins_panel() %}
{% for gene in variant.genes %} {% for transcript in gene.transcripts %} {% endfor %} {% endfor %}
Gene Transcript Protein SWISS PROT Sift Polyphen Pfam ProSite Smart
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {{ transcript.transcript_id }} {{ transcript.protein_id if transcript.protein_id }} {% if transcript.swiss_prot != 'unknown' %} {{ transcript.swiss_prot }} {% else %} {{ transcript.swiss_prot }} {% endif %} {{ transcript.sift_prediction }} {{ transcript.polyphen_prediction }} {{ transcript.pfam_domain if transcript.pfam_domain }} {{ transcript.prosite_profile if transcript.prosite_profile }} {{ transcript.smart_domain if transcript.smart_domain }}
{% endmacro %} {% macro modal_sanger() %}
{% endmacro %} {% macro modal_cancel_sanger() %}
{% endmacro %} {% macro external_links() %}
{% for gene in variant.genes %}
External links: {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
Ensembl HPA STRING UCSC {% if gene.entrez_link %} Entrez {% endif %} SPANR Reactome Expr. Atlas ClinGen Alamut Protein Paint {% if variant.chromosome == 'MT' %} MitoMap {% endif %}
{% endfor %}
{% endmacro %} {% macro acmg_form(selected=None) %}
{% for option in ACMG_OPTIONS %} {% endfor %}
{% endmacro %} {% macro acmg_classification_item(data) %} {% set current_variant = (data.variant_specific == variant._id) %}
  • {{ data.classification.label }} {{ data.classification.short }} {% if not current_variant %} {{ data.case.display_name }} {% endif %}
    {{ data.user_name }} on {{ data.created_at.date() }} {% if current_variant %} {% endif %}
  • {% endmacro %} {% block scripts %} {{ super() }} {% endblock %}