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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: 16-29384067-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=29384067&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 29384067,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001310137.5",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPB11",
"gene_hgnc_id": 37453,
"hgvs_c": "c.865C>G",
"hgvs_p": "p.Leu289Val",
"transcript": "NM_001310137.5",
"protein_id": "NP_001297066.2",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 1161,
"cds_start": 865,
"cds_end": null,
"cds_length": 3486,
"cdna_start": 3612,
"cdna_end": null,
"cdna_length": 6369,
"mane_select": "ENST00000698511.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPB11",
"gene_hgnc_id": 37453,
"hgvs_c": "c.865C>G",
"hgvs_p": "p.Leu289Val",
"transcript": "ENST00000698511.1",
"protein_id": "ENSP00000513761.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 1161,
"cds_start": 865,
"cds_end": null,
"cds_length": 3486,
"cdna_start": 3612,
"cdna_end": null,
"cdna_length": 6369,
"mane_select": "NM_001310137.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPB11",
"gene_hgnc_id": 37453,
"hgvs_c": "c.865C>G",
"hgvs_p": "p.Leu289Val",
"transcript": "ENST00000524087.5",
"protein_id": "ENSP00000430853.1",
"transcript_support_level": 5,
"aa_start": 289,
"aa_end": null,
"aa_length": 1161,
"cds_start": 865,
"cds_end": null,
"cds_length": 3486,
"cdna_start": 940,
"cdna_end": null,
"cdna_length": 3653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPB11",
"gene_hgnc_id": 37453,
"hgvs_c": "c.865C>G",
"hgvs_p": "p.Leu289Val",
"transcript": "XM_047434576.1",
"protein_id": "XP_047290532.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 1122,
"cds_start": 865,
"cds_end": null,
"cds_length": 3369,
"cdna_start": 865,
"cdna_end": null,
"cdna_length": 3648,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPB11",
"gene_hgnc_id": 37453,
"hgvs_c": "c.865C>G",
"hgvs_p": "p.Leu289Val",
"transcript": "XM_047434577.1",
"protein_id": "XP_047290533.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 913,
"cds_start": 865,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 865,
"cdna_end": null,
"cdna_length": 3019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPB11",
"gene_hgnc_id": 37453,
"hgvs_c": "c.808C>G",
"hgvs_p": "p.Leu270Val",
"transcript": "XM_047434578.1",
"protein_id": "XP_047290534.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 894,
"cds_start": 808,
"cds_end": null,
"cds_length": 2685,
"cdna_start": 1235,
"cdna_end": null,
"cdna_length": 3389,
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "RRN3P2",
"gene_hgnc_id": 37619,
"hgvs_c": "n.899+19008G>C",
"hgvs_p": null,
"transcript": "ENST00000769491.1",
"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": 1220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NPIPB11",
"gene_hgnc_id": 37453,
"dbsnp": "rs202027988",
"frequency_reference_population": 0.0025528017,
"hom_count_reference_population": 162,
"allele_count_reference_population": 3049,
"gnomad_exomes_af": 0.00251566,
"gnomad_genomes_af": 0.00301245,
"gnomad_exomes_ac": 2780,
"gnomad_genomes_ac": 269,
"gnomad_exomes_homalt": 159,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.020652711391448975,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.057,
"revel_prediction": "Benign",
"alphamissense_score": 0.2017,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.289,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001310137.5",
"gene_symbol": "NPIPB11",
"hgnc_id": 37453,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.865C>G",
"hgvs_p": "p.Leu289Val"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000769491.1",
"gene_symbol": "RRN3P2",
"hgnc_id": 37619,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.899+19008G>C",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}