{% extends "layout.html" %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }} {% endblock %} {% set pheno_hpos = [] %} {% set pheno_features = [] %} {% block top_nav %}
  • {{ institute.display_name }}
  • {{ case.display_name }}
  • {% if cancer %} {{ variant.variant_type|capitalize }} cancer variants {% else %} {{ variant.variant_type|capitalize }} SNV and INDELs {% endif %}
  • {% endblock %} {% block content_main %}

    Clinvar submission page


    Clinvar is a freely accessible archive of clinically relevant variants. Contributing to this database helps improving data sharing and increasing the number of genetic diagnoses worldwide.
    The form present on this page mirrors the fields on the Clinvar submission spreadsheets. After collecting all the required fields for submitting one or more variants to Clinvar, the info is subsequently processed into comma separated files, ready to be uploaded in the submission process.
    Link to the official Clinvar documentation.

    {% if 'phenotype_groups' in case and case.phenotype_groups|length >0 or 'phenotype_terms' in case and case.phenotype_terms|length >0 %} {% for pheno in case.phenotype_terms if not pheno.phenotype_id in pheno_hpos %} {% do pheno_hpos.append(pheno.phenotype_id) %} {% do pheno_features.append(pheno.feature) %} {% endfor %} {% for pheno in case.phenotype_groups if not pheno.phenotype_id in pheno_hpos %} {% do pheno_hpos.append(pheno.phenotype_id) %} {% do pheno_features.append(pheno.feature) %} {% endfor %}

    {{ panel_variant('main_var') }}
    {% else %} Can't submit to clinvar without specifying at least a phenotype for this case! Back to case {% endif %}
    {% endblock %} {% macro panel_variant(var_type) %} {% for pinned in pinned_vars %} {% if var_type=='main_var' and pinned._id == variant._id or var_type=='other_vars' and not pinned._id == variant._id %} {% if pinned.category != 'sv' %} {% endif %}

    {% if pinned.category == 'snv' %} snv {% else %} sv {% endif %} {% if pinned.simple_id|length > 25 and pinned.cytoband_start %} #Variant --> {{ pinned.sub_category+"("+pinned.chromosome+pinned.cytoband_start+"-"+pinned.end_chrom+pinned.cytoband_end+")" }} {% elif pinned.simple_id|length > 25 %} #Variant --> {{ pinned.sub_category+"(chr."+pinned.chromosome+")" }} {% else %} #Variant --> {{ pinned.simple_id }} {% endif %}
    {% if pinned.category == 'snv' %} {% endif %} {% if pinned.simple_id|length > 25 and pinned.cytoband_start %} {% elif pinned.simple_id|length > 25 %} {% else %} {% endif %} {% if pinned.category == 'snv' %} {% endif %} {% if pinned.dbsnp_id and pinned.category == 'snv'%} {% endif %}
    Gene symbol(s): {% set gene_symbols = [] %} {% for gene in pinned.genes %} {% do gene_symbols.append(gene.hgnc_symbol) %} {% if pinned.genes|length == 1 %} {{ pinned.genes[0].hgnc_symbol }}
    {% else %} {% for gene in pinned.genes %} {{ gene.hgnc_symbol+";" }} {% endfor %} {% endif %} {% endfor %}
    Coordinates:{{ pinned.sub_category + "(" + pinned.chromosome+pinned.cytoband_start+"-"+pinned.end_chrom+pinned.cytoband_end +"), length:"+ pinned.length|string }}chr{{ pinned.chromosome }}:{{pinned.position}} ({{ pinned.sub_category }})chr{{ pinned.chromosome }}:{{pinned.position}} ({{ pinned.reference }} -> {{ pinned.alternative }})
    Transcripts & HGVS:
    (optional)
    {% for gene in pinned.genes %} {% for transcript in gene.transcripts %} {% if transcript.refseq_id and transcript.coding_sequence_name %}
    {% endif %} {% endfor %} {% endfor %}
    Variant model of inheritance
    {% for model in pinned.genetic_models|sort %} {{ model }} {% endfor %}
    var. identifier
    Clinical significance:
    Date last evaluated
    Functional consequence:
    (based on experimental evidence, leave blank if unsure)
    Condition HPO term(s):
    (associated with the variant)
    {% for hpo in pheno_hpos %} {{ hpo }}
    {% endfor %}
    Additional comments describing condition:
    {% if pinned.category == 'sv' %}
    {% if pinned.sub_category == 'del'%} {%else%} {% endif %}
    Type of structural variant:
    Reference copy number
    Breakpoint 1
    Breakpoint 2


    Outer start*
    Inner start*
    Inner stop*
    Outer stop*
    * How to display uncertainty of breakpoint locations
    Comments on this variant
    {% endif %} More optional fields
    Assertion method:
    Assertion citation
    Clinical significance citations
    (with identifier)
    Method
    Comments on clinical significance
    Drug response condition(s)
    {% for individual in case.individuals %} {% if individual.phenotype == 2 %} {% for sample in pinned.samples %} {% if sample.display_name == individual.display_name and sample.genotype_call != '0/0' and sample.genotype_call != './.' %}
    {% if pinned.simple_id|length > 25 and pinned.cytoband_start%}
    Subject {{ individual.display_name }}, variant {{ pinned.sub_category+"("+pinned.chromosome+pinned.cytoband_start+"-"+pinned.end_chrom+pinned.cytoband_end+")" }}
    {% elif pinned.simple_id|length > 25 %}
    Subject {{ individual.display_name }}, variant {{ pinned.sub_category+"(chr."+pinned.chromosome+")" }}
    {% else %}
    Subject {{ individual.display_name }}, variant {{ pinned.simple_id }}
    {% endif %}
    Affected? Ethnicity
    sex {% if individual.sex == "1" %} male {% else %} female {% endif %} Age:
    Allele origin Zygosity {% for sample in pinned.samples %} {% if sample.display_name == individual.display_name %} ({{ sample.genotype_call }})
    {% endif %} {% endfor %}
    {% if pinned.category == 'sv' %}
    Structural variant analysis:
    {% endif %}
    Was {{individual.display_name}} a proband?
    Family history?
    Was this a secondary finding?
    Mosaicism observed?
    Co-occurrences same gene
    Co-occurrences other genes
    Date variant was reported to submitter
    Tissue where genetic material was extracted from
    Subject phenotypes
    (HPO terms. ONLY if different from variant's HPO terms)
    Comments on clinical features
    Evidence citations
    Testing laboratory
    Platform type
    Platform name {% if individual.analysis_type == 'wes' %} {% else %} {% endif %}
    Method
    Method purpose
    Method citations
    {% elif sample.display_name == individual.display_name %} No case data harboring this allelic variant!
    {% endif %} {% endfor %} {% endif %} {% endfor %} {% endif %} {% endfor %} {% endmacro %} {% block scripts %} {% endblock %}