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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: 5-71564883-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=71564883&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 71564883,
"ref": "T",
"alt": "G",
"effect": "stop_lost",
"transcript": "ENST00000358731.9",
"consequences": [
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_lost"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "c.7873T>G",
"hgvs_p": "p.Ter2625Gluext*?",
"transcript": "NM_018429.3",
"protein_id": "NP_060899.2",
"transcript_support_level": null,
"aa_start": 2625,
"aa_end": null,
"aa_length": 2624,
"cds_start": 7873,
"cds_end": null,
"cds_length": 7875,
"cdna_start": 8100,
"cdna_end": null,
"cdna_length": 11037,
"mane_select": "ENST00000358731.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_lost"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "c.7873T>G",
"hgvs_p": "p.Ter2625Gluext*?",
"transcript": "ENST00000358731.9",
"protein_id": "ENSP00000351575.4",
"transcript_support_level": 1,
"aa_start": 2625,
"aa_end": null,
"aa_length": 2624,
"cds_start": 7873,
"cds_end": null,
"cds_length": 7875,
"cdna_start": 8100,
"cdna_end": null,
"cdna_length": 11037,
"mane_select": "NM_018429.3",
"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": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "n.*239T>G",
"hgvs_p": null,
"transcript": "ENST00000525844.1",
"protein_id": "ENSP00000432404.1",
"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": 4997,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "n.*239T>G",
"hgvs_p": null,
"transcript": "ENST00000525844.1",
"protein_id": "ENSP00000432404.1",
"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": 4997,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_lost"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "c.7867T>G",
"hgvs_p": "p.Ter2623Gluext*?",
"transcript": "XM_011543511.4",
"protein_id": "XP_011541813.1",
"transcript_support_level": null,
"aa_start": 2623,
"aa_end": null,
"aa_length": 2622,
"cds_start": 7867,
"cds_end": null,
"cds_length": 7869,
"cdna_start": 8094,
"cdna_end": null,
"cdna_length": 11031,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_lost"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "c.7354T>G",
"hgvs_p": "p.Ter2452Gluext*?",
"transcript": "XM_011543512.3",
"protein_id": "XP_011541814.1",
"transcript_support_level": null,
"aa_start": 2452,
"aa_end": null,
"aa_length": 2451,
"cds_start": 7354,
"cds_end": null,
"cds_length": 7356,
"cdna_start": 7581,
"cdna_end": null,
"cdna_length": 10518,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "n.*823T>G",
"hgvs_p": null,
"transcript": "ENST00000514903.7",
"protein_id": "ENSP00000421910.3",
"transcript_support_level": 5,
"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": 5511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "n.*823T>G",
"hgvs_p": null,
"transcript": "ENST00000514903.7",
"protein_id": "ENSP00000421910.3",
"transcript_support_level": 5,
"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": 5511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "c.*2097T>G",
"hgvs_p": null,
"transcript": "XM_047417373.1",
"protein_id": "XP_047273329.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2584,
"cds_start": -4,
"cds_end": null,
"cds_length": 7755,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13016,
"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": 40,
"intron_rank": 38,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "c.7743+2363T>G",
"hgvs_p": null,
"transcript": "XM_017009630.2",
"protein_id": "XP_016865119.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2624,
"cds_start": -4,
"cds_end": null,
"cds_length": 7875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10438,
"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": 40,
"intron_rank": 38,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "c.7743+2363T>G",
"hgvs_p": null,
"transcript": "XM_017009631.2",
"protein_id": "XP_016865120.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2624,
"cds_start": -4,
"cds_end": null,
"cds_length": 7875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8618,
"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": 41,
"intron_rank": 38,
"intron_rank_end": null,
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"hgvs_c": "c.7743+2363T>G",
"hgvs_p": null,
"transcript": "XM_047417372.1",
"protein_id": "XP_047273328.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2624,
"cds_start": -4,
"cds_end": null,
"cds_length": 7875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BDP1",
"gene_hgnc_id": 13652,
"dbsnp": "rs199721728",
"frequency_reference_population": 0.00062527077,
"hom_count_reference_population": 3,
"allele_count_reference_population": 990,
"gnomad_exomes_af": 0.000632427,
"gnomad_genomes_af": 0.000558043,
"gnomad_exomes_ac": 905,
"gnomad_genomes_ac": 85,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.699999988079071,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.7,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.616,
"phylop100way_prediction": "Benign",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM4,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000358731.9",
"gene_symbol": "BDP1",
"hgnc_id": 13652,
"effects": [
"stop_lost"
],
"inheritance_mode": "AR",
"hgvs_c": "c.7873T>G",
"hgvs_p": "p.Ter2625Gluext*?"
}
],
"clinvar_disease": " autosomal recessive 112,Hearing loss,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LB:2",
"phenotype_combined": "Hearing loss, autosomal recessive 112|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}