{% 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 %}
Position {{ variant.chromosome }}:{{ variant.position }} | Change {{ variant.reference }} → {{ variant.alternative }} |
Gene | Region | Function |
---|---|---|
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} | {{ gene.region_annotation }} | {{ gene.functional_annotation|truncate(20, True) }} |
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 case.bam_files %} View alignment {% else %} BAM file missing {% endif %} | {% if config.SQLALCHEMY_DATABASE_URI %} {% for gene in variant.genes %}{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} | {% endfor %} {% endif %}
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 '') }} |
Gene | OMIM | Manual | {% for gene in variant.incomplete_penetrance %}
---|---|---|
{{ gene.hgnc_symbol }} | {% if gene.omim %} yes {% else %} no {% endif %} | {% if gene.manual %} yes {% else %} no {% endif %} |
Gene | Phenotype | Inheritance model |
---|---|---|
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} | {{ disease_term.description }} | {{ disease_term.inheritance|join(', ') }} |
Sample | Genotype (GT) | Allele depth (AD) | Genotype quality (GQ) | ||
---|---|---|---|---|---|
Reference | Alternative | ||||
{{ sample.display_name }} | {{ sample.genotype_call }} | {% if sample.allele_depths %} {% for number in sample.allele_depths %}{{ number }} | {% endfor %} {% else %}N/A | N/A | {% endif %}{{ sample.genotype_quality }} |
Single sample case: {{ case.individuals.0.display_name }}
{% else %} {{ case.madeline_info|safe }} {% endif %}{{ result.category|replace('_', ' ') }} | {% endfor %}
---|
{{ result.score }} | {% 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 |
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 }} |
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 '') }} |
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 }} |