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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: 5-138381576-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=138381576&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 138381576,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000314358.10",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3B",
"gene_hgnc_id": 1337,
"hgvs_c": "c.766G>A",
"hgvs_p": "p.Ala256Thr",
"transcript": "NM_016604.4",
"protein_id": "NP_057688.3",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 1761,
"cds_start": 766,
"cds_end": null,
"cds_length": 5286,
"cdna_start": 877,
"cdna_end": null,
"cdna_length": 6724,
"mane_select": "ENST00000314358.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3B",
"gene_hgnc_id": 1337,
"hgvs_c": "c.766G>A",
"hgvs_p": "p.Ala256Thr",
"transcript": "ENST00000314358.10",
"protein_id": "ENSP00000326563.5",
"transcript_support_level": 1,
"aa_start": 256,
"aa_end": null,
"aa_length": 1761,
"cds_start": 766,
"cds_end": null,
"cds_length": 5286,
"cdna_start": 877,
"cdna_end": null,
"cdna_length": 6724,
"mane_select": "NM_016604.4",
"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": 5,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3B",
"gene_hgnc_id": 1337,
"hgvs_c": "n.574G>A",
"hgvs_p": null,
"transcript": "ENST00000510866.5",
"protein_id": "ENSP00000425186.1",
"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": 6324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3B",
"gene_hgnc_id": 1337,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Ala212Thr",
"transcript": "XM_011543488.3",
"protein_id": "XP_011541790.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1717,
"cds_start": 634,
"cds_end": null,
"cds_length": 5154,
"cdna_start": 661,
"cdna_end": null,
"cdna_length": 6508,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3B",
"gene_hgnc_id": 1337,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Ala208Thr",
"transcript": "XM_011543489.3",
"protein_id": "XP_011541791.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 1713,
"cds_start": 622,
"cds_end": null,
"cds_length": 5142,
"cdna_start": 2859,
"cdna_end": null,
"cdna_length": 8706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3B",
"gene_hgnc_id": 1337,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Ala208Thr",
"transcript": "XM_047417313.1",
"protein_id": "XP_047273269.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 1713,
"cds_start": 622,
"cds_end": null,
"cds_length": 5142,
"cdna_start": 1781,
"cdna_end": null,
"cdna_length": 7628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3B",
"gene_hgnc_id": 1337,
"hgvs_c": "c.766G>A",
"hgvs_p": "p.Ala256Thr",
"transcript": "XM_005272018.5",
"protein_id": "XP_005272075.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 1561,
"cds_start": 766,
"cds_end": null,
"cds_length": 4686,
"cdna_start": 877,
"cdna_end": null,
"cdna_length": 6124,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3B",
"gene_hgnc_id": 1337,
"hgvs_c": "c.19G>A",
"hgvs_p": "p.Ala7Thr",
"transcript": "XM_017009584.2",
"protein_id": "XP_016865073.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 1512,
"cds_start": 19,
"cds_end": null,
"cds_length": 4539,
"cdna_start": 345,
"cdna_end": null,
"cdna_length": 6192,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM3B",
"gene_hgnc_id": 1337,
"hgvs_c": "n.455G>A",
"hgvs_p": null,
"transcript": "ENST00000512928.1",
"protein_id": null,
"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": 627,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KDM3B",
"gene_hgnc_id": 1337,
"dbsnp": "rs6865472",
"frequency_reference_population": 0.9970062,
"hom_count_reference_population": 796510,
"allele_count_reference_population": 1597487,
"gnomad_exomes_af": 0.998427,
"gnomad_genomes_af": 0.983486,
"gnomad_exomes_ac": 1447649,
"gnomad_genomes_ac": 149838,
"gnomad_exomes_homalt": 722753,
"gnomad_genomes_homalt": 73757,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 8.278509540105006e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.024,
"revel_prediction": "Benign",
"alphamissense_score": 0.0602,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.678,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BA1",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000314358.10",
"gene_symbol": "KDM3B",
"hgnc_id": 1337,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.766G>A",
"hgvs_p": "p.Ala256Thr"
}
],
"clinvar_disease": "Diets-Jongmans syndrome",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "Diets-Jongmans syndrome",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}