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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: 12-21022906-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=21022906&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 21022906,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "NM_001371097.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "SLCO1B3-SLCO1B7",
"gene_hgnc_id": 54403,
"hgvs_c": "c.1866-44413C>T",
"hgvs_p": null,
"transcript": "ENST00000540229.1",
"protein_id": "ENSP00000441269.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 748,
"cds_start": null,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000540229.1"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLCO1B3-SLCO1B7",
"gene_hgnc_id": 54403,
"hgvs_c": "c.538C>T",
"hgvs_p": "p.Leu180Phe",
"transcript": "ENST00000381541.7",
"protein_id": "ENSP00000370952.3",
"transcript_support_level": 2,
"aa_start": 180,
"aa_end": null,
"aa_length": 687,
"cds_start": 538,
"cds_end": null,
"cds_length": 2064,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000381541.7"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124902894",
"gene_hgnc_id": null,
"hgvs_c": "c.397C>T",
"hgvs_p": "p.Leu133Phe",
"transcript": "XM_047429949.1",
"protein_id": "XP_047285905.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 400,
"cds_start": 397,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429949.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "SLCO1B3-SLCO1B7",
"gene_hgnc_id": 54403,
"hgvs_c": "c.1866-44413C>T",
"hgvs_p": null,
"transcript": "NM_001371097.1",
"protein_id": "NP_001358026.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 748,
"cds_start": null,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001371097.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLCO1B7",
"gene_hgnc_id": 32934,
"hgvs_c": "n.538C>T",
"hgvs_p": null,
"transcript": "ENST00000648739.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "transcribed_unprocessed_pseudogene",
"feature": "ENST00000648739.1"
}
],
"gene_symbol": "SLCO1B3-SLCO1B7",
"gene_hgnc_id": 54403,
"dbsnp": "rs555291179",
"frequency_reference_population": 0.000016737687,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.0000164257,
"gnomad_genomes_af": 0.0000197368,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7201622724533081,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.435,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2043,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.155,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001371097.1",
"gene_symbol": "SLCO1B3-SLCO1B7",
"hgnc_id": 54403,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1866-44413C>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "XM_047429949.1",
"gene_symbol": "LOC124902894",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.397C>T",
"hgvs_p": "p.Leu133Phe"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000648739.1",
"gene_symbol": "SLCO1B7",
"hgnc_id": 32934,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "n.538C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}