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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: 6-139373259-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=139373259&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 139373259,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_006079.5",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CITED2",
"gene_hgnc_id": 1987,
"hgvs_c": "c.686T>C",
"hgvs_p": "p.Met229Thr",
"transcript": "NM_006079.5",
"protein_id": "NP_006070.2",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 270,
"cds_start": 686,
"cds_end": null,
"cds_length": 813,
"cdna_start": 930,
"cdna_end": null,
"cdna_length": 2382,
"mane_select": "ENST00000367651.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CITED2",
"gene_hgnc_id": 1987,
"hgvs_c": "c.686T>C",
"hgvs_p": "p.Met229Thr",
"transcript": "ENST00000367651.4",
"protein_id": "ENSP00000356623.2",
"transcript_support_level": 1,
"aa_start": 229,
"aa_end": null,
"aa_length": 270,
"cds_start": 686,
"cds_end": null,
"cds_length": 813,
"cdna_start": 930,
"cdna_end": null,
"cdna_length": 2382,
"mane_select": "NM_006079.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CITED2",
"gene_hgnc_id": 1987,
"hgvs_c": "c.701T>C",
"hgvs_p": "p.Met234Thr",
"transcript": "NM_001168389.3",
"protein_id": "NP_001161861.2",
"transcript_support_level": null,
"aa_start": 234,
"aa_end": null,
"aa_length": 275,
"cds_start": 701,
"cds_end": null,
"cds_length": 828,
"cdna_start": 776,
"cdna_end": null,
"cdna_length": 2228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CITED2",
"gene_hgnc_id": 1987,
"hgvs_c": "c.701T>C",
"hgvs_p": "p.Met234Thr",
"transcript": "ENST00000537332.2",
"protein_id": "ENSP00000444198.2",
"transcript_support_level": 3,
"aa_start": 234,
"aa_end": null,
"aa_length": 275,
"cds_start": 701,
"cds_end": null,
"cds_length": 828,
"cdna_start": 776,
"cdna_end": null,
"cdna_length": 1780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CITED2",
"gene_hgnc_id": 1987,
"hgvs_c": "c.686T>C",
"hgvs_p": "p.Met229Thr",
"transcript": "NM_001168388.3",
"protein_id": "NP_001161860.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 270,
"cds_start": 686,
"cds_end": null,
"cds_length": 813,
"cdna_start": 793,
"cdna_end": null,
"cdna_length": 2245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CITED2",
"gene_hgnc_id": 1987,
"hgvs_c": "c.686T>C",
"hgvs_p": "p.Met229Thr",
"transcript": "ENST00000536159.2",
"protein_id": "ENSP00000442831.1",
"transcript_support_level": 3,
"aa_start": 229,
"aa_end": null,
"aa_length": 270,
"cds_start": 686,
"cds_end": null,
"cds_length": 813,
"cdna_start": 793,
"cdna_end": null,
"cdna_length": 1797,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000226571",
"gene_hgnc_id": null,
"hgvs_c": "n.510-55822A>G",
"hgvs_p": null,
"transcript": "ENST00000650173.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2413,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000226571",
"gene_hgnc_id": null,
"hgvs_c": "n.420-55822A>G",
"hgvs_p": null,
"transcript": "ENST00000775570.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1504,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000226571",
"gene_hgnc_id": null,
"hgvs_c": "n.435-8722A>G",
"hgvs_p": null,
"transcript": "ENST00000775571.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CITED2",
"gene_hgnc_id": 1987,
"dbsnp": "rs1327285914",
"frequency_reference_population": 0.0000061955643,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000615663,
"gnomad_genomes_af": 0.00000656944,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.20175465941429138,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.145,
"revel_prediction": "Benign",
"alphamissense_score": 0.9518,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.718,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2_Supporting",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2_Supporting"
],
"verdict": "Likely_benign",
"transcript": "NM_006079.5",
"gene_symbol": "CITED2",
"hgnc_id": 1987,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.686T>C",
"hgvs_p": "p.Met229Thr"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000650173.1",
"gene_symbol": "ENSG00000226571",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.510-55822A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}