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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: 2-86456519-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=86456519&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 86456519,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000312912.10",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "c.634A>G",
"hgvs_p": "p.Ile212Val",
"transcript": "NM_018433.6",
"protein_id": "NP_060903.2",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1321,
"cds_start": 634,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 738,
"cdna_end": null,
"cdna_length": 4667,
"mane_select": "ENST00000312912.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "c.634A>G",
"hgvs_p": "p.Ile212Val",
"transcript": "ENST00000312912.10",
"protein_id": "ENSP00000323659.5",
"transcript_support_level": 1,
"aa_start": 212,
"aa_end": null,
"aa_length": 1321,
"cds_start": 634,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 738,
"cdna_end": null,
"cdna_length": 4667,
"mane_select": "NM_018433.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "c.634A>G",
"hgvs_p": "p.Ile212Val",
"transcript": "ENST00000409064.5",
"protein_id": "ENSP00000386516.1",
"transcript_support_level": 1,
"aa_start": 212,
"aa_end": null,
"aa_length": 1321,
"cds_start": 634,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 692,
"cdna_end": null,
"cdna_length": 4621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "c.634A>G",
"hgvs_p": "p.Ile212Val",
"transcript": "NM_001146688.2",
"protein_id": "NP_001140160.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1321,
"cds_start": 634,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 692,
"cdna_end": null,
"cdna_length": 4621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "c.634A>G",
"hgvs_p": "p.Ile212Val",
"transcript": "ENST00000409556.5",
"protein_id": "ENSP00000386660.1",
"transcript_support_level": 5,
"aa_start": 212,
"aa_end": null,
"aa_length": 1321,
"cds_start": 634,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 999,
"cdna_end": null,
"cdna_length": 4928,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "c.634A>G",
"hgvs_p": "p.Ile212Val",
"transcript": "XM_047445101.1",
"protein_id": "XP_047301057.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1321,
"cds_start": 634,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 713,
"cdna_end": null,
"cdna_length": 4642,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "c.634A>G",
"hgvs_p": "p.Ile212Val",
"transcript": "XM_047445102.1",
"protein_id": "XP_047301058.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1321,
"cds_start": 634,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 4583,
"cdna_end": null,
"cdna_length": 8512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "c.634A>G",
"hgvs_p": "p.Ile212Val",
"transcript": "XM_047445103.1",
"protein_id": "XP_047301059.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1321,
"cds_start": 634,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 833,
"cdna_end": null,
"cdna_length": 4762,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "c.634A>G",
"hgvs_p": "p.Ile212Val",
"transcript": "XM_047445104.1",
"protein_id": "XP_047301060.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1321,
"cds_start": 634,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 745,
"cdna_end": null,
"cdna_length": 4674,
"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": 6,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "n.634A>G",
"hgvs_p": null,
"transcript": "ENST00000441719.5",
"protein_id": "ENSP00000394691.1",
"transcript_support_level": 2,
"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": 8741,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "n.441A>G",
"hgvs_p": null,
"transcript": "ENST00000463013.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 577,
"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": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"hgvs_c": "n.87A>G",
"hgvs_p": null,
"transcript": "ENST00000488971.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 975,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KDM3A",
"gene_hgnc_id": 20815,
"dbsnp": "rs2030259",
"frequency_reference_population": 0.75963545,
"hom_count_reference_population": 467664,
"allele_count_reference_population": 1220444,
"gnomad_exomes_af": 0.755556,
"gnomad_genomes_af": 0.798928,
"gnomad_exomes_ac": 1099718,
"gnomad_genomes_ac": 120726,
"gnomad_exomes_homalt": 418859,
"gnomad_genomes_homalt": 48805,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 5.481292646436486e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.055,
"revel_prediction": "Benign",
"alphamissense_score": 0.0548,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.187,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000312912.10",
"gene_symbol": "KDM3A",
"hgnc_id": 20815,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.634A>G",
"hgvs_p": "p.Ile212Val"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}