BioMCP

{% if section_only -%}
# {{ section_header }}
{% else -%}
# {{ gene }}{% if hgvs_p %} {{ hgvs_p }}{% endif %}{% if rsid %} ({{ rsid }}){% endif %}

rsID: {% if rsid %}{{ rsid }}{% else %}Not reported{% endif %}
ID: {{ id }}
{% if hgvs_p %}Protein: {{ hgvs_p }}{% endif %}
{% if hgvs_c %}cDNA: {{ hgvs_c }}{% endif %}
{% if consequence %}Consequence: {{ consequence }}{% endif %}
{% if cosmic_id %}COSMIC: {{ cosmic_id }}{% endif %}
{% if significance %}Significance: {{ significance }}{% endif %}
{% endif -%}
{% if show_prediction_section and prediction -%}
## AlphaGenome Prediction

| Score | Value | Interpretation |
|---|---|---|
| Expression LFC | {% if prediction.expression_lfc is not none %}{{ prediction.expression_lfc | score }}{% else %}-{% endif %} | {% if expression_interpretation %}{{ expression_interpretation }}{% else %}-{% endif %} |
| Splice Score | {% if prediction.splice_score is not none %}{{ prediction.splice_score | score }}{% else %}-{% endif %} | {% if splice_interpretation %}{{ splice_interpretation }}{% else %}-{% endif %} |
| Chromatin | {% if prediction.chromatin_score is not none %}{{ prediction.chromatin_score | score }}{% else %}-{% endif %} | {% if chromatin_interpretation %}{{ chromatin_interpretation }}{% else %}-{% endif %} |

Top Affected Gene (Ensembl ID when available): {% if prediction.top_gene %}{{ prediction.top_gene }}{% else %}-{% endif %}
Note: AlphaGenome reports this field as a gene-level identifier from its model output.
{% endif -%}
{% if show_clinvar_section and (conditions or clinvar_id or clinvar_conditions) -%}
## ClinVar
{% if clinvar_conditions -%}
Conditions ({% if clinvar_condition_reports %}{{ clinvar_condition_reports }}{% else %}{{ clinvar_conditions | length }}{% endif %} reports):
{% for row in clinvar_conditions -%}
- {{ row.condition }} ({{ row.reports }} report{% if row.reports != 1 %}s{% endif %})
{% endfor -%}
{% elif conditions -%}
- Conditions: {{ conditions | join(", ") }}
{% endif -%}
{% if clinvar_review_stars is not none -%}
- Review: {{ clinvar_review_stars }} star(s){% if clinvar_review_status %} ({{ clinvar_review_status }}){% endif %}
{% endif -%}
{% if clinvar_id -%}
- Variant ID: {{ clinvar_id }}
{% endif -%}
{% endif -%}
{% if show_conservation_section -%}
## Conservation
{% if conservation -%}
| Metric | Score |
|---|---|
| phyloP (100-way vertebrate) | {% if conservation.phylop_100way_vertebrate is defined and conservation.phylop_100way_vertebrate is not none %}{{ conservation.phylop_100way_vertebrate | score }}{% else %}-{% endif %} |
| phyloP (470-way mammalian) | {% if conservation.phylop_470way_mammalian is defined and conservation.phylop_470way_mammalian is not none %}{{ conservation.phylop_470way_mammalian | score }}{% else %}-{% endif %} |
| phastCons (100-way vertebrate) | {% if conservation.phastcons_100way_vertebrate is defined and conservation.phastcons_100way_vertebrate is not none %}{{ conservation.phastcons_100way_vertebrate | score }}{% else %}-{% endif %} |
| phastCons (470-way mammalian) | {% if conservation.phastcons_470way_mammalian is defined and conservation.phastcons_470way_mammalian is not none %}{{ conservation.phastcons_470way_mammalian | score }}{% else %}-{% endif %} |
| GERP++ RS | {% if conservation.gerp_rs is defined and conservation.gerp_rs is not none %}{{ conservation.gerp_rs | score }}{% else %}-{% endif %} |
{% else -%}
No conservation scores reported.
{% endif -%}
{% endif -%}
{% if show_predictions_section -%}
## Expanded Predictions
{% if expanded_predictions -%}
| Tool | Score | Prediction |
|---|---|---|
{% for p in expanded_predictions -%}
| {{ p.tool }} | {% if p.score is defined and p.score is not none %}{{ p.score | score }}{% else %}-{% endif %} | {% if p.prediction %}{{ p.prediction }}{% else %}-{% endif %} |
{% endfor -%}
{% else -%}
No expanded prediction scores reported.
{% endif -%}
{% endif -%}
{% if show_population_section -%}
## Population
{% if population -%}
- Dataset: {{ population.dataset }}
- Variant ID: {{ population.variant_id }}
{% if population.af is defined and population.af is not none %}- AF: {{ population.af | af }}{% endif %}
{% if population.populations -%}
| Population (gnomAD API) | AF |
|---|---|
{% for p in population.populations -%}
| {{ p.population }} | {{ p.af | af }} |
{% endfor -%}
{% endif -%}
{% else -%}
{% if gnomad_af %}- gnomAD AF: {{ gnomad_af | af }}{% else %}- gnomAD AF: Not reported{% endif %}
{% if gnomad_subpopulations -%}
- Sub-populations: {% for p in gnomad_subpopulations -%}{{ p.population }} {{ p.af | af }}{% if not loop.last %}, {% endif %}{% endfor %}
{% endif -%}
{% endif -%}
{% if population_breakdown -%}
{% if population_breakdown.populations -%}
| Population (MyVariant cached) | AF |
|---|---|
{% for p in population_breakdown.populations -%}
| {{ p.population }} | {{ p.af | af }} |
{% endfor -%}
{% endif -%}
{% if population_breakdown.exac_af is defined and population_breakdown.exac_af is not none %}- ExAC AF: {{ population_breakdown.exac_af | af }}{% endif %}
{% if population_breakdown.exac_nontcga_af is defined and population_breakdown.exac_nontcga_af is not none %}- ExAC non-TCGA AF: {{ population_breakdown.exac_nontcga_af | af }}{% endif %}
{% endif -%}
{% if (not population) and (not population_breakdown) and (not gnomad_af) and (not gnomad_subpopulations) -%}
No population data reported.
{% endif -%}
{% endif -%}
{% if show_cosmic_section -%}
## COSMIC
{% if cosmic_id or cosmic_context -%}
{% if cosmic_id %}- COSMIC ID: {{ cosmic_id }}{% endif %}
{% if cosmic_context and cosmic_context.mut_freq is defined and cosmic_context.mut_freq is not none %}- Mutation frequency: {{ cosmic_context.mut_freq | score }}{% endif %}
{% if cosmic_context and cosmic_context.tumor_site %}- Tumor site: {{ cosmic_context.tumor_site }}{% endif %}
{% if cosmic_context and cosmic_context.mut_nt %}- Mutation nucleotide: {{ cosmic_context.mut_nt }}{% endif %}
{% else -%}
No COSMIC context reported.
{% endif -%}
{% endif -%}
{% if show_cgi_section -%}
## CGI Drug Associations
{% if cgi_associations -%}
| Drug | Association | Tumor Type | Evidence |
|---|---|---|---|
{% for row in cgi_associations -%}
| {{ row.drug }} | {{ row.association or "-" }} | {{ row.tumor_type or "-" }} | {{ row.evidence_level or "-" }} |
{% endfor -%}
{% else -%}
No CGI drug associations reported.
{% endif -%}
{% endif -%}
{% if show_civic_section -%}
## CIViC
{% if civic -%}
{% if civic.cached_evidence -%}
### Cached Evidence (MyVariant)
| Evidence | Type | Level | Disease | Therapies |
|---|---|---|---|---|
{% for row in civic.cached_evidence -%}
| {{ row.name }} | {{ row.evidence_type }} | {{ row.evidence_level }} | {{ row.disease or "-" }} | {% if row.therapies %}{{ row.therapies | join(", ") }}{% else %}-{% endif %} |
{% endfor -%}
{% endif -%}
{% if civic.graphql -%}
### GraphQL Context
- Evidence Items: {{ civic.graphql.evidence_total_count }}
- Assertions: {{ civic.graphql.assertion_total_count }}
{% if civic.graphql.assertions -%}
| Assertion | AMP Level | Disease | Therapies |
|---|---|---|---|
{% for row in civic.graphql.assertions -%}
| {{ row.name }} | {{ row.amp_level or "-" }} | {{ row.disease or "-" }} | {% if row.therapies %}{{ row.therapies | join(", ") }}{% else %}-{% endif %} |
{% endfor -%}
{% elif civic.graphql.evidence_items -%}
| Evidence | Level | Disease | Therapies |
|---|---|---|---|
{% for row in civic.graphql.evidence_items -%}
| {{ row.name }} | {{ row.evidence_level }} | {{ row.disease or "-" }} | {% if row.therapies %}{{ row.therapies | join(", ") }}{% else %}-{% endif %} |
{% endfor -%}
{% endif -%}
{% endif -%}
{% if (not civic.cached_evidence) and (not civic.graphql) -%}
No CIViC records returned for this variant.
{% endif -%}
{% else -%}
No CIViC records returned for this variant.
{% endif -%}
{% endif -%}
{% if not section_only and (cadd_score or sift_pred or polyphen_pred) -%}
## Predictions
{% if cadd_score -%}
- CADD: {{ cadd_score }}
{% endif -%}
{% if sift_pred -%}
- SIFT: {{ sift_pred }}
{% endif -%}
{% if polyphen_pred -%}
- PolyPhen: {{ polyphen_pred }}
{% endif -%}
{% endif -%}
{% if show_cbioportal_section -%}
## cBioPortal
{% if cancer_frequencies -%}
| Cancer Type | Samples | Frequency |
|---|---|---|
{% for cf in cancer_frequencies -%}
| {{ cf.cancer_type }} | {{ cf.sample_count }} | {{ cf.frequency | af }} |
{% endfor %}
{% else -%}
No cBioPortal frequency data available.
{% endif -%}
{% endif -%}
{% if show_gwas_section -%}
## GWAS
{% if gwas -%}
| rsID | Trait | p-value | Effect | Confidence | Risk AF | Risk Allele | Study | PMID | Author |
|---|---|---|---|---|---|---|---|---|---|
{% for row in gwas -%}
| {{ row.rsid }} | {{ row.trait_name or "-" }} | {% if row.p_value is defined and row.p_value is not none %}{{ row.p_value | pval }}{% else %}-{% endif %} | {% if row.effect_size is defined and row.effect_size is not none %}{{ row.effect_type or "effect" }} {{ row.effect_size | score }}{% else %}-{% endif %} | {{ row.confidence_interval or "-" }} | {% if row.risk_allele_frequency is defined and row.risk_allele_frequency is not none %}{{ row.risk_allele_frequency | af }}{% else %}-{% endif %} | {{ row.risk_allele or "-" }} | {{ row.study_accession or "-" }} | {{ row.pmid or "-" }} | {{ row.author or "-" }} |
{% endfor -%}
{% else -%}
No GWAS associations found for this variant.
{% endif -%}
{% endif -%}
{% if sections -%}
Sections: {{ sections }}
{% endif -%}
{% if related -%}
Related: {{ related }}
{% endif -%}