{% extends "layout.html" %} {% from "utils.html" import comments_panel, activity_panel %} {% from "variants/utils.html" import compounds_table %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }} {% endblock %} {% block top_nav %}
  • {{ institute.display_name }}
  • {{ case.display_name }}
  • {{ variant.variant_type|capitalize }} SNV and INDELs
  • {% endblock %} {% block top_nav_right %} {% if config['MAIL_USERNAME'] %} {# Email setting must be setup #}
  • {{ sanger_button() }}
  • {% endif %}
  • {{ pin_button() }}
  • {{ causative_button() }}
  • {{ 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() }}
    {% set has_pedigree = case.madeline_info and case.individuals|length > 1 %}
    {{ comments_panel(institute, case, current_user, comments, variant_id=variant._id) }}
    {{ gtcall_panel() }}
    {% if has_pedigree %}
    {{ pedigree_panel() }}
    {% endif %}
    {% if variant.compounds %}
    {{ compounds_panel() }}
    {% endif %}
    {{ rankscore_panel() }}
    {{ overlapping_panel() }}
    {{ genes_panel() }}
    {{ transcripts_panel() }}
    {{ proteins_panel() }}
    {{ external_links() }}
    {{ activity_panel(events|reverse) }}
    {% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {{ modal_sanger() }} {% endif %} {% endblock %} {% macro sanger_button() %} {% if variant.sanger_ordered %} {% if variant.validation %} {% 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 %}
    {% else %}
    {% endif %} {% endmacro %} {% macro matching_variants() %}
    Matching causatives from other cases
    {% endmacro %} {% macro panel_basics() %}
    Basics
    Position {{ variant.chromosome }}:{{ variant.position }} 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) }}
    {% 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 }}
    Gene coverage
    {% if config.SQLALCHEMY_DATABASE_URI %} {% for gene in variant.genes %} {% endfor %} {% endif %}
    {% if case.bam_files %} View alignment {% else %} BAM file missing {% endif %} {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
    {% endmacro %} {% macro transcript_overview() %}
    Transcript overview
    {% for gene in variant.genes %} {% for transcript in gene.transcripts|selectattr('refseq_ids') %} {% endfor %} {% endfor %}
    Gene Transcript HGVS Description
    {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {% if transcript.is_canonical %} C {% endif %} {{ transcript.refseq_ids|join(', ') }} {{ (transcript.protein_sequence_name or '') }} {{ (transcript.coding_sequence_name or '') }}
    Disease associated transcripts
    {% for transcript_str in variant.disease_associated_transcripts %} {{ transcript_str }} {% else %} No transcripts {% endfor %}
    {% endmacro %} {% macro frequency_list() %}
    Frequency
    {% if config.LOQUSDB_SETTINGS %}
    Local observations
    Local observations (archived)
    {% endif %}
    {% endmacro %} {% macro severity_list() %}
    Severity
    Conservation
    {% endmacro %} {% macro inheritance_panel() %}
    Inheritance models
    Incomplete penetrance
    {% for gene in variant.incomplete_penetrance %} {% endfor %}
    Gene OMIM Manual
    {{ gene.hgnc_symbol }} {% if gene.omim %} yes {% else %} no {% endif %} {% if gene.manual %} yes {% else %} no {% endif %}
    {% endmacro %} {% macro omim_phenotypes() %}
    OMIM
    {% for gene in variant.genes %} {% for disease_term in gene.disease_terms %} {% endfor %} {% endfor %}
    Gene Phenotype Inheritance model
    {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {{ disease_term.description }} {{ disease_term.inheritance|join(', ') }}
    {% endmacro %} {% macro gtcall_panel() %}
    GT call
    {% 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 pedigree_panel() %}
    Pedigree
    {% if case.individuals|length == 1 %}

    Single sample case: {{ case.individuals.0.display_name }}

    {% else %} {{ case.madeline_info|safe }} {% endif %}
    {% 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 Combined score Rank score Length Region Function
    {{ sv_variant.display_name|truncate(20, True) }} {{ sv_variant.hgnc_symbols|join(', ')|truncate(40, True) }} {{ 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 %} {% for refseq in transcript.refseq_links %} {{ refseq.id }} {% endfor %} {{ 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 '') }}
    {% 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 external_links() %}
    {% for gene in variant.genes %}
    External links: {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
    {% endfor %}
    {% endmacro %} {% block scripts %} {{ super() }} {% endblock %}