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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: Y-19730686-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=Y&pos=19730686&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "Y",
"pos": 19730686,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000317961.9",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null,
"transcript": "NM_004653.5",
"protein_id": "NP_004644.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1539,
"cds_start": -4,
"cds_end": null,
"cds_length": 4620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6825,
"mane_select": "ENST00000317961.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null,
"transcript": "ENST00000317961.9",
"protein_id": "ENSP00000322408.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1539,
"cds_start": -4,
"cds_end": null,
"cds_length": 4620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6825,
"mane_select": "NM_004653.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null,
"transcript": "ENST00000541639.5",
"protein_id": "ENSP00000444293.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1570,
"cds_start": -4,
"cds_end": null,
"cds_length": 4713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1200+1086G>A",
"hgvs_p": null,
"transcript": "ENST00000382806.6",
"protein_id": "ENSP00000372256.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1482,
"cds_start": -4,
"cds_end": null,
"cds_length": 4449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null,
"transcript": "NM_001146705.2",
"protein_id": "NP_001140177.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1570,
"cds_start": -4,
"cds_end": null,
"cds_length": 4713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1200+1086G>A",
"hgvs_p": null,
"transcript": "NM_001146706.2",
"protein_id": "NP_001140178.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1482,
"cds_start": -4,
"cds_end": null,
"cds_length": 4449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6654,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1248+1086G>A",
"hgvs_p": null,
"transcript": "ENST00000440077.5",
"protein_id": "ENSP00000398543.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1475,
"cds_start": -4,
"cds_end": null,
"cds_length": 4429,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1236+1086G>A",
"hgvs_p": null,
"transcript": "ENST00000447300.1",
"protein_id": "ENSP00000416377.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 424,
"cds_start": -4,
"cds_end": null,
"cds_length": 1276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null,
"transcript": "XM_011531468.4",
"protein_id": "XP_011529770.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1513,
"cds_start": -4,
"cds_end": null,
"cds_length": 4542,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6747,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1236+1086G>A",
"hgvs_p": null,
"transcript": "XM_005262560.4",
"protein_id": "XP_005262617.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1494,
"cds_start": -4,
"cds_end": null,
"cds_length": 4485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1236+1086G>A",
"hgvs_p": null,
"transcript": "XM_047442763.1",
"protein_id": "XP_047298719.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1468,
"cds_start": -4,
"cds_end": null,
"cds_length": 4407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null,
"transcript": "XM_005262561.4",
"protein_id": "XP_005262618.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1462,
"cds_start": -4,
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"cds_length": 4389,
"cdna_start": null,
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"cdna_length": 6594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null,
"transcript": "XM_047442764.1",
"protein_id": "XP_047298720.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1436,
"cds_start": -4,
"cds_end": null,
"cds_length": 4311,
"cdna_start": null,
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"cdna_length": 6516,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1236+1086G>A",
"hgvs_p": null,
"transcript": "XM_047442765.1",
"protein_id": "XP_047298721.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1236+1086G>A",
"hgvs_p": null,
"transcript": "XM_047442766.1",
"protein_id": "XP_047298722.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1391,
"cds_start": -4,
"cds_end": null,
"cds_length": 4176,
"cdna_start": null,
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"cdna_length": 6381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null,
"transcript": "XM_047442767.1",
"protein_id": "XP_047298723.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 20,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null,
"transcript": "XM_047442768.1",
"protein_id": "XP_047298724.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 888,
"cds_start": -4,
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"cds_length": 2667,
"cdna_start": null,
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"cdna_length": 3459,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null,
"transcript": "XM_047442769.1",
"protein_id": "XP_047298725.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 781,
"cds_start": -4,
"cds_end": null,
"cds_length": 2346,
"cdna_start": null,
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"cdna_length": 2517,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null,
"transcript": "XM_047442770.1",
"protein_id": "XP_047298726.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 686,
"cds_start": -4,
"cds_end": null,
"cds_length": 2061,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2253,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KDM5D",
"gene_hgnc_id": 11115,
"dbsnp": "rs2032640",
"frequency_reference_population": 0.0065368153,
"hom_count_reference_population": 197,
"allele_count_reference_population": 197,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00653682,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 197,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9200000166893005,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.92,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.145,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000317961.9",
"gene_symbol": "KDM5D",
"hgnc_id": 11115,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1371+1086G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}