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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: 12-20883599-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=20883599&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 20883599,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000540229.1",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLCO1B3",
"gene_hgnc_id": 10961,
"hgvs_c": "c.1679T>C",
"hgvs_p": "p.Val560Ala",
"transcript": "NM_019844.4",
"protein_id": "NP_062818.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 702,
"cds_start": 1679,
"cds_end": null,
"cds_length": 2109,
"cdna_start": 1919,
"cdna_end": null,
"cdna_length": 3013,
"mane_select": "ENST00000381545.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLCO1B3",
"gene_hgnc_id": 10961,
"hgvs_c": "c.1679T>C",
"hgvs_p": "p.Val560Ala",
"transcript": "ENST00000381545.8",
"protein_id": "ENSP00000370956.4",
"transcript_support_level": 2,
"aa_start": 560,
"aa_end": null,
"aa_length": 702,
"cds_start": 1679,
"cds_end": null,
"cds_length": 2109,
"cdna_start": 1919,
"cdna_end": null,
"cdna_length": 3013,
"mane_select": "NM_019844.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLCO1B3-SLCO1B7",
"gene_hgnc_id": 54403,
"hgvs_c": "c.1679T>C",
"hgvs_p": "p.Val560Ala",
"transcript": "ENST00000540229.1",
"protein_id": "ENSP00000441269.1",
"transcript_support_level": 2,
"aa_start": 560,
"aa_end": null,
"aa_length": 748,
"cds_start": 1679,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 1744,
"cdna_end": null,
"cdna_length": 2451,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLCO1B3",
"gene_hgnc_id": 10961,
"hgvs_c": "c.1679T>C",
"hgvs_p": "p.Val560Ala",
"transcript": "ENST00000261196.6",
"protein_id": "ENSP00000261196.2",
"transcript_support_level": 1,
"aa_start": 560,
"aa_end": null,
"aa_length": 702,
"cds_start": 1679,
"cds_end": null,
"cds_length": 2109,
"cdna_start": 1746,
"cdna_end": null,
"cdna_length": 2840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLCO1B3-SLCO1B7",
"gene_hgnc_id": 54403,
"hgvs_c": "c.1679T>C",
"hgvs_p": "p.Val560Ala",
"transcript": "NM_001371097.1",
"protein_id": "NP_001358026.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 748,
"cds_start": 1679,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 1744,
"cdna_end": null,
"cdna_length": 3428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLCO1B3",
"gene_hgnc_id": 10961,
"hgvs_c": "c.1595T>C",
"hgvs_p": "p.Val532Ala",
"transcript": "NM_001349920.2",
"protein_id": "NP_001336849.1",
"transcript_support_level": null,
"aa_start": 532,
"aa_end": null,
"aa_length": 674,
"cds_start": 1595,
"cds_end": null,
"cds_length": 2025,
"cdna_start": 1721,
"cdna_end": null,
"cdna_length": 2815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLCO1B3",
"gene_hgnc_id": 10961,
"hgvs_c": "c.1151T>C",
"hgvs_p": "p.Val384Ala",
"transcript": "ENST00000544370.1",
"protein_id": "ENSP00000443225.1",
"transcript_support_level": 5,
"aa_start": 384,
"aa_end": null,
"aa_length": 479,
"cds_start": 1151,
"cds_end": null,
"cds_length": 1440,
"cdna_start": 1151,
"cdna_end": null,
"cdna_length": 1771,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 14,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SLCO1B3-SLCO1B7",
"gene_hgnc_id": 54403,
"hgvs_c": "c.359+25028T>C",
"hgvs_p": null,
"transcript": "ENST00000381541.7",
"protein_id": "ENSP00000370952.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 687,
"cds_start": -4,
"cds_end": null,
"cds_length": 2064,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2268,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLCO1B3-SLCO1B7",
"gene_hgnc_id": 54403,
"dbsnp": "rs12299012",
"frequency_reference_population": 0.0013302179,
"hom_count_reference_population": 29,
"allele_count_reference_population": 2103,
"gnomad_exomes_af": 0.00069014,
"gnomad_genomes_af": 0.00733671,
"gnomad_exomes_ac": 986,
"gnomad_genomes_ac": 1117,
"gnomad_exomes_homalt": 12,
"gnomad_genomes_homalt": 17,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008660465478897095,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.115,
"revel_prediction": "Benign",
"alphamissense_score": 0.3912,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.853,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.11,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000540229.1",
"gene_symbol": "SLCO1B3-SLCO1B7",
"hgnc_id": 54403,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1679T>C",
"hgvs_p": "p.Val560Ala"
},
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000381545.8",
"gene_symbol": "SLCO1B3",
"hgnc_id": 10961,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1679T>C",
"hgvs_p": "p.Val560Ala"
}
],
"clinvar_disease": "Rotor syndrome,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1 B:1",
"phenotype_combined": "not provided|Rotor syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}