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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: M-9997-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=M&pos=9997&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "M",
"pos": 9997,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000000000",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNG",
"gene_hgnc_id": 7486,
"hgvs_c": "c.7T>C",
"hgvs_p": "p.Leu3Leu",
"transcript": "unassigned_transcript_4807",
"protein_id": null,
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 21,
"cds_start": 7,
"cds_end": null,
"cds_length": 68,
"cdna_start": 7,
"cdna_end": null,
"cdna_length": 68,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TG",
"gene_hgnc_id": 7486,
"hgvs_c": "n.7T>C",
"hgvs_p": null,
"transcript": "ENST00000387429.1",
"protein_id": null,
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 68,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-ND3",
"gene_hgnc_id": 7458,
"hgvs_c": "c.-62T>C",
"hgvs_p": null,
"transcript": "ENST00000361227.2",
"protein_id": "ENSP00000355206.2",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 114,
"cds_start": -4,
"cds_end": null,
"cds_length": 346,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-CO3",
"gene_hgnc_id": 7422,
"hgvs_c": "c.*7T>C",
"hgvs_p": null,
"transcript": "ENST00000362079.2",
"protein_id": "ENSP00000354982.2",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 260,
"cds_start": -4,
"cds_end": null,
"cds_length": 784,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ND3",
"gene_hgnc_id": 7458,
"hgvs_c": "c.-62T>C",
"hgvs_p": null,
"transcript": "unassigned_transcript_4808",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 114,
"cds_start": -4,
"cds_end": null,
"cds_length": 346,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX3",
"gene_hgnc_id": 7422,
"hgvs_c": "c.*7T>C",
"hgvs_p": null,
"transcript": "unassigned_transcript_4806",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 260,
"cds_start": -4,
"cds_end": null,
"cds_length": 784,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TRNG",
"gene_hgnc_id": 7486,
"dbsnp": "rs121434475",
"frequency_reference_population": 0,
"hom_count_reference_population": 1,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 16.95240020751953,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "Mitotip",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.316,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": 16.95240020751953,
"mitotip_prediction": "Pathogenic",
"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP7",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP7"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "TRNG",
"hgnc_id": 7486,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.7T>C",
"hgvs_p": "p.Leu3Leu"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000387429.1",
"gene_symbol": "MT-TG",
"hgnc_id": 7486,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.7T>C",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000361227.2",
"gene_symbol": "MT-ND3",
"hgnc_id": 7458,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial,AR",
"hgvs_c": "c.-62T>C",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000362079.2",
"gene_symbol": "MT-CO3",
"hgnc_id": 7422,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial,AD,AR",
"hgvs_c": "c.*7T>C",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "ND3",
"hgnc_id": 7458,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial,AR",
"hgvs_c": "c.-62T>C",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "COX3",
"hgnc_id": 7422,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial,AD,AR",
"hgvs_c": "c.*7T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Mitochondrial disease,Primary familial hypertrophic cardiomyopathy,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Unspecified-patient-from-clinical-lab,MHCM,Primary familial hypertrophic cardiomyopathy|not specified|Mitochondrial disease",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}