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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: 19-9854485-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=9854485&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 9854485,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001304347.2",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"hgvs_c": "c.1066G>A",
"hgvs_p": "p.Glu356Lys",
"transcript": "NM_058164.4",
"protein_id": "NP_477512.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 454,
"cds_start": 1066,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264833.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_058164.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"hgvs_c": "c.1066G>A",
"hgvs_p": "p.Glu356Lys",
"transcript": "ENST00000264833.9",
"protein_id": "ENSP00000264833.3",
"transcript_support_level": 1,
"aa_start": 356,
"aa_end": null,
"aa_length": 454,
"cds_start": 1066,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_058164.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264833.9"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"hgvs_c": "c.1138G>A",
"hgvs_p": "p.Glu380Lys",
"transcript": "NM_001304347.2",
"protein_id": "NP_001291276.1",
"transcript_support_level": null,
"aa_start": 380,
"aa_end": null,
"aa_length": 478,
"cds_start": 1138,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001304347.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"hgvs_c": "c.1138G>A",
"hgvs_p": "p.Glu380Lys",
"transcript": "ENST00000593091.2",
"protein_id": "ENSP00000465809.2",
"transcript_support_level": 5,
"aa_start": 380,
"aa_end": null,
"aa_length": 478,
"cds_start": 1138,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000593091.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"hgvs_c": "c.1057G>A",
"hgvs_p": "p.Glu353Lys",
"transcript": "ENST00000971550.1",
"protein_id": "ENSP00000641609.1",
"transcript_support_level": null,
"aa_start": 353,
"aa_end": null,
"aa_length": 451,
"cds_start": 1057,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971550.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"hgvs_c": "c.919G>A",
"hgvs_p": "p.Glu307Lys",
"transcript": "ENST00000882493.1",
"protein_id": "ENSP00000552552.1",
"transcript_support_level": null,
"aa_start": 307,
"aa_end": null,
"aa_length": 405,
"cds_start": 919,
"cds_end": null,
"cds_length": 1218,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882493.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"hgvs_c": "c.832G>A",
"hgvs_p": "p.Glu278Lys",
"transcript": "NM_001304348.2",
"protein_id": "NP_001291277.1",
"transcript_support_level": null,
"aa_start": 278,
"aa_end": null,
"aa_length": 376,
"cds_start": 832,
"cds_end": null,
"cds_length": 1131,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001304348.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"hgvs_c": "c.832G>A",
"hgvs_p": "p.Glu278Lys",
"transcript": "ENST00000590841.5",
"protein_id": "ENSP00000464877.1",
"transcript_support_level": 2,
"aa_start": 278,
"aa_end": null,
"aa_length": 376,
"cds_start": 832,
"cds_end": null,
"cds_length": 1131,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000590841.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"hgvs_c": "c.592G>A",
"hgvs_p": "p.Glu198Lys",
"transcript": "ENST00000923214.1",
"protein_id": "ENSP00000593273.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 296,
"cds_start": 592,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923214.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"hgvs_c": "c.862G>A",
"hgvs_p": "p.Glu288Lys",
"transcript": "XM_047439713.1",
"protein_id": "XP_047295669.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 386,
"cds_start": 862,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439713.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"hgvs_c": "n.*471G>A",
"hgvs_p": null,
"transcript": "ENST00000592448.1",
"protein_id": "ENSP00000466018.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000592448.1"
}
],
"gene_symbol": "OLFM2",
"gene_hgnc_id": 17189,
"dbsnp": "rs2046297014",
"frequency_reference_population": 0.0000034206746,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342067,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5703549981117249,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.601,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1843,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.623,
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001304347.2",
"gene_symbol": "OLFM2",
"hgnc_id": 17189,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1138G>A",
"hgvs_p": "p.Glu380Lys"
}
],
"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
}