{% extends "layout_bs4.html" %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }} {% endblock %} {% set pheno_hpos = [] %} {% set pheno_features = [] %} {% set pheno_omims = [] %} {% 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 %} {% for omim_id in case.diagnosis_phenotypes %} {% do pheno_omims.append(omim_id) %} {% endfor %} {% block top_nav %} {% 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 pheno_hpos|length >0 or pheno_omims|length >0 %}

{{ 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'%} {% set dbsnp_id = pinned.dbsnp_id.split(':')[0] %} {% 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:
Comment on clinical significance
Date last evaluated
Functional consequence:
(based on experimental evidence, leave blank if unsure)
Condition HPO term(s):
(associated to the variant)
{% for hpo in pheno_hpos %} {{ hpo }} - {{pheno_features[loop.index -1]}}
{% else %} No preselected HPO term available. {% endfor %}
OMIM diagnoses:
(associated to the variant)
{% for omim in pheno_omims %} {{ omim }}
{% else %} No preselected OMIM diagnosis available. {% 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
Clinical features
(HPO terms. ONLY if different from variant's HPO terms)
{% for hpo in pheno_hpos %} {{ hpo }} - {{pheno_features[loop.index -1]}}
{% else %} No preselected HPO term available. {% endfor %}
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 %} {{ super() }} {% endblock %}