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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: 4-39225027-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=39225027&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 39225027,
"ref": "C",
"alt": "G",
"effect": "stop_gained",
"transcript": "ENST00000399820.8",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "c.1623C>G",
"hgvs_p": "p.Tyr541*",
"transcript": "NM_025132.4",
"protein_id": "NP_079408.3",
"transcript_support_level": null,
"aa_start": 541,
"aa_end": null,
"aa_length": 1342,
"cds_start": 1623,
"cds_end": null,
"cds_length": 4029,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 4395,
"mane_select": "ENST00000399820.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "c.1623C>G",
"hgvs_p": "p.Tyr541*",
"transcript": "ENST00000399820.8",
"protein_id": "ENSP00000382717.3",
"transcript_support_level": 1,
"aa_start": 541,
"aa_end": null,
"aa_length": 1342,
"cds_start": 1623,
"cds_end": null,
"cds_length": 4029,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 4395,
"mane_select": "NM_025132.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "c.1143C>G",
"hgvs_p": "p.Tyr381*",
"transcript": "NM_001317924.2",
"protein_id": "NP_001304853.1",
"transcript_support_level": null,
"aa_start": 381,
"aa_end": null,
"aa_length": 1182,
"cds_start": 1143,
"cds_end": null,
"cds_length": 3549,
"cdna_start": 1536,
"cdna_end": null,
"cdna_length": 4279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "c.1623C>G",
"hgvs_p": "p.Tyr541*",
"transcript": "XM_011513724.2",
"protein_id": "XP_011512026.1",
"transcript_support_level": null,
"aa_start": 541,
"aa_end": null,
"aa_length": 1346,
"cds_start": 1623,
"cds_end": null,
"cds_length": 4041,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 4407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "c.1557C>G",
"hgvs_p": "p.Tyr519*",
"transcript": "XM_011513725.3",
"protein_id": "XP_011512027.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 1324,
"cds_start": 1557,
"cds_end": null,
"cds_length": 3975,
"cdna_start": 1586,
"cdna_end": null,
"cdna_length": 4341,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "c.1557C>G",
"hgvs_p": "p.Tyr519*",
"transcript": "XM_047416030.1",
"protein_id": "XP_047271986.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 1320,
"cds_start": 1557,
"cds_end": null,
"cds_length": 3963,
"cdna_start": 1586,
"cdna_end": null,
"cdna_length": 4329,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "c.1623C>G",
"hgvs_p": "p.Tyr541*",
"transcript": "XM_047416031.1",
"protein_id": "XP_047271987.1",
"transcript_support_level": null,
"aa_start": 541,
"aa_end": null,
"aa_length": 1195,
"cds_start": 1623,
"cds_end": null,
"cds_length": 3588,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 5387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "c.1623C>G",
"hgvs_p": "p.Tyr541*",
"transcript": "XM_047416032.1",
"protein_id": "XP_047271988.1",
"transcript_support_level": null,
"aa_start": 541,
"aa_end": null,
"aa_length": 1191,
"cds_start": 1623,
"cds_end": null,
"cds_length": 3576,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 5375,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "c.1143C>G",
"hgvs_p": "p.Tyr381*",
"transcript": "XM_047416033.1",
"protein_id": "XP_047271989.1",
"transcript_support_level": null,
"aa_start": 381,
"aa_end": null,
"aa_length": 1186,
"cds_start": 1143,
"cds_end": null,
"cds_length": 3561,
"cdna_start": 1306,
"cdna_end": null,
"cdna_length": 4061,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "c.1623C>G",
"hgvs_p": "p.Tyr541*",
"transcript": "XM_047416034.1",
"protein_id": "XP_047271990.1",
"transcript_support_level": null,
"aa_start": 541,
"aa_end": null,
"aa_length": 969,
"cds_start": 1623,
"cds_end": null,
"cds_length": 2910,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 2978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "c.1623C>G",
"hgvs_p": "p.Tyr541*",
"transcript": "XM_047416035.1",
"protein_id": "XP_047271991.1",
"transcript_support_level": null,
"aa_start": 541,
"aa_end": null,
"aa_length": 761,
"cds_start": 1623,
"cds_end": null,
"cds_length": 2286,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 2377,
"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": 14,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "n.*1204C>G",
"hgvs_p": null,
"transcript": "ENST00000506869.5",
"protein_id": "ENSP00000424319.1",
"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": 4249,
"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": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "n.621C>G",
"hgvs_p": null,
"transcript": "ENST00000512095.5",
"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": 3095,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "n.*1204C>G",
"hgvs_p": null,
"transcript": "ENST00000506869.5",
"protein_id": "ENSP00000424319.1",
"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": 4249,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"hgvs_c": "n.41-3531C>G",
"hgvs_p": null,
"transcript": "ENST00000511729.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "WDR19",
"gene_hgnc_id": 18340,
"dbsnp": "rs771148519",
"frequency_reference_population": 0.000010264398,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.00000995241,
"gnomad_genomes_af": 0.0000131499,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5899999737739563,
"computational_prediction_selected": "Pathogenic",
"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": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.377,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000399820.8",
"gene_symbol": "WDR19",
"hgnc_id": 18340,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1623C>G",
"hgvs_p": "p.Tyr541*"
}
],
"clinvar_disease": "Asphyxiating thoracic dystrophy 5,Cranioectodermal dysplasia,Cranioectodermal dysplasia 4,Nephronophthisis 13,Senior-Loken syndrome 8,Spermatogenic failure 72",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "Cranioectodermal dysplasia|Spermatogenic failure 72;Asphyxiating thoracic dystrophy 5;Nephronophthisis 13;Senior-Loken syndrome 8;Cranioectodermal dysplasia 4|Asphyxiating thoracic dystrophy 5;Senior-Loken syndrome 8",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}