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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: 12-121857429-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=121857429&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 121857429,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000289004.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPD",
"gene_hgnc_id": 5147,
"hgvs_c": "c.97A>G",
"hgvs_p": "p.Thr33Ala",
"transcript": "NM_002150.3",
"protein_id": "NP_002141.2",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 393,
"cds_start": 97,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 133,
"cdna_end": null,
"cdna_length": 1419,
"mane_select": "ENST00000289004.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPD",
"gene_hgnc_id": 5147,
"hgvs_c": "c.97A>G",
"hgvs_p": "p.Thr33Ala",
"transcript": "ENST00000289004.8",
"protein_id": "ENSP00000289004.4",
"transcript_support_level": 1,
"aa_start": 33,
"aa_end": null,
"aa_length": 393,
"cds_start": 97,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 133,
"cdna_end": null,
"cdna_length": 1419,
"mane_select": "NM_002150.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPD",
"gene_hgnc_id": 5147,
"hgvs_c": "n.453A>G",
"hgvs_p": null,
"transcript": "ENST00000535114.1",
"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": 582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPD",
"gene_hgnc_id": 5147,
"hgvs_c": "n.155A>G",
"hgvs_p": null,
"transcript": "ENST00000542159.2",
"protein_id": null,
"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": 780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPD",
"gene_hgnc_id": 5147,
"hgvs_c": "c.-21A>G",
"hgvs_p": null,
"transcript": "NM_001171993.2",
"protein_id": "NP_001165464.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 354,
"cds_start": -4,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPD",
"gene_hgnc_id": 5147,
"hgvs_c": "c.-21A>G",
"hgvs_p": null,
"transcript": "ENST00000543163.5",
"protein_id": "ENSP00000441677.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 354,
"cds_start": -4,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1709,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TIALD",
"gene_hgnc_id": 56938,
"hgvs_c": "n.140+1037T>C",
"hgvs_p": null,
"transcript": "ENST00000750773.1",
"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": 288,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TIALD",
"gene_hgnc_id": 56938,
"hgvs_c": "n.371-190T>C",
"hgvs_p": null,
"transcript": "ENST00000750774.1",
"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": 737,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TIALD",
"gene_hgnc_id": 56938,
"hgvs_c": "n.346+783T>C",
"hgvs_p": null,
"transcript": "ENST00000750775.1",
"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": 489,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TIALD",
"gene_hgnc_id": 56938,
"hgvs_c": "n.395-190T>C",
"hgvs_p": null,
"transcript": "XR_002957437.2",
"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": 757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HPD",
"gene_hgnc_id": 5147,
"dbsnp": "rs1154510",
"frequency_reference_population": 0.8661744,
"hom_count_reference_population": 604622,
"allele_count_reference_population": 1392067,
"gnomad_exomes_af": 0.864765,
"gnomad_genomes_af": 0.879649,
"gnomad_exomes_ac": 1258202,
"gnomad_genomes_ac": 133865,
"gnomad_exomes_homalt": 545475,
"gnomad_genomes_homalt": 59147,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.000002099031007674057,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.192,
"revel_prediction": "Benign",
"alphamissense_score": 0.042,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.228,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000289004.8",
"gene_symbol": "HPD",
"hgnc_id": 5147,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown,AD",
"hgvs_c": "c.97A>G",
"hgvs_p": "p.Thr33Ala"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000750773.1",
"gene_symbol": "TIALD",
"hgnc_id": 56938,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.140+1037T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Hawkinsinuria,Tyrosinemia type III,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:7",
"phenotype_combined": "Hawkinsinuria|Tyrosinemia type III;Hawkinsinuria|Tyrosinemia type III|not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}