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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: 19-49878529-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49878529&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 49878529,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_024682.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D17",
"gene_hgnc_id": 25699,
"hgvs_c": "c.152T>A",
"hgvs_p": "p.Val51Glu",
"transcript": "NM_024682.3",
"protein_id": "NP_078958.2",
"transcript_support_level": null,
"aa_start": 51,
"aa_end": null,
"aa_length": 648,
"cds_start": 152,
"cds_end": null,
"cds_length": 1947,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 2095,
"mane_select": "ENST00000221543.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D17",
"gene_hgnc_id": 25699,
"hgvs_c": "c.152T>A",
"hgvs_p": "p.Val51Glu",
"transcript": "ENST00000221543.10",
"protein_id": "ENSP00000221543.4",
"transcript_support_level": 1,
"aa_start": 51,
"aa_end": null,
"aa_length": 648,
"cds_start": 152,
"cds_end": null,
"cds_length": 1947,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 2095,
"mane_select": "NM_024682.3",
"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": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D17",
"gene_hgnc_id": 25699,
"hgvs_c": "n.152T>A",
"hgvs_p": null,
"transcript": "ENST00000594996.5",
"protein_id": "ENSP00000469010.1",
"transcript_support_level": 1,
"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": 1161,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D17",
"gene_hgnc_id": 25699,
"hgvs_c": "c.53T>A",
"hgvs_p": "p.Val18Glu",
"transcript": "NM_001168222.2",
"protein_id": "NP_001161694.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 615,
"cds_start": 53,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 75,
"cdna_end": null,
"cdna_length": 1996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D17",
"gene_hgnc_id": 25699,
"hgvs_c": "c.53T>A",
"hgvs_p": "p.Val18Glu",
"transcript": "ENST00000535102.6",
"protein_id": "ENSP00000446323.1",
"transcript_support_level": 2,
"aa_start": 18,
"aa_end": null,
"aa_length": 615,
"cds_start": 53,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 111,
"cdna_end": null,
"cdna_length": 2025,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D17",
"gene_hgnc_id": 25699,
"hgvs_c": "c.86T>A",
"hgvs_p": "p.Val29Glu",
"transcript": "ENST00000599049.6",
"protein_id": "ENSP00000472647.1",
"transcript_support_level": 5,
"aa_start": 29,
"aa_end": null,
"aa_length": 479,
"cds_start": 86,
"cds_end": null,
"cds_length": 1440,
"cdna_start": 87,
"cdna_end": null,
"cdna_length": 1742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D17",
"gene_hgnc_id": 25699,
"hgvs_c": "c.152T>A",
"hgvs_p": "p.Val51Glu",
"transcript": "XM_047439444.1",
"protein_id": "XP_047295400.1",
"transcript_support_level": null,
"aa_start": 51,
"aa_end": null,
"aa_length": 565,
"cds_start": 152,
"cds_end": null,
"cds_length": 1698,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 1774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D17",
"gene_hgnc_id": 25699,
"hgvs_c": "c.152T>A",
"hgvs_p": "p.Val51Glu",
"transcript": "XM_011527317.4",
"protein_id": "XP_011525619.1",
"transcript_support_level": null,
"aa_start": 51,
"aa_end": null,
"aa_length": 501,
"cds_start": 152,
"cds_end": null,
"cds_length": 1506,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 1829,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D17",
"gene_hgnc_id": 25699,
"hgvs_c": "n.198T>A",
"hgvs_p": null,
"transcript": "ENST00000598789.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 556,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D17",
"gene_hgnc_id": 25699,
"hgvs_c": "n.-21T>A",
"hgvs_p": null,
"transcript": "ENST00000596243.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKT1S1",
"gene_hgnc_id": 28426,
"hgvs_c": "c.-367A>T",
"hgvs_p": null,
"transcript": "NM_001278160.2",
"protein_id": "NP_001265089.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 256,
"cds_start": -4,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKT1S1",
"gene_hgnc_id": 28426,
"hgvs_c": "c.-367A>T",
"hgvs_p": null,
"transcript": "ENST00000391834.6",
"protein_id": "ENSP00000375710.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 256,
"cds_start": -4,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1849,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKT1S1",
"gene_hgnc_id": 28426,
"hgvs_c": "c.-367A>T",
"hgvs_p": null,
"transcript": "ENST00000391830.1",
"protein_id": "ENSP00000375706.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 107,
"cds_start": -4,
"cds_end": null,
"cds_length": 326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKT1S1",
"gene_hgnc_id": 28426,
"hgvs_c": "n.-173A>T",
"hgvs_p": null,
"transcript": "ENST00000482622.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 328,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.-178A>T",
"hgvs_p": null,
"transcript": "ENST00000629179.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TBC1D17",
"gene_hgnc_id": 25699,
"dbsnp": "rs1258476854",
"frequency_reference_population": 0.0000013681444,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136814,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2562296986579895,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.158,
"revel_prediction": "Benign",
"alphamissense_score": 0.1315,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.786,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_024682.3",
"gene_symbol": "TBC1D17",
"hgnc_id": 25699,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.152T>A",
"hgvs_p": "p.Val51Glu"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001278160.2",
"gene_symbol": "AKT1S1",
"hgnc_id": 28426,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-367A>T",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000629179.1",
"gene_symbol": "PNKP",
"hgnc_id": 9154,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "n.-178A>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
}