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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: 4-39224985-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=39224985&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 39224985,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000399820.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"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.1581C>A",
"hgvs_p": "p.Thr527Thr",
"transcript": "NM_025132.4",
"protein_id": "NP_079408.3",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1342,
"cds_start": 1581,
"cds_end": null,
"cds_length": 4029,
"cdna_start": 1610,
"cdna_end": null,
"cdna_length": 4395,
"mane_select": "ENST00000399820.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"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.1581C>A",
"hgvs_p": "p.Thr527Thr",
"transcript": "ENST00000399820.8",
"protein_id": "ENSP00000382717.3",
"transcript_support_level": 1,
"aa_start": 527,
"aa_end": null,
"aa_length": 1342,
"cds_start": 1581,
"cds_end": null,
"cds_length": 4029,
"cdna_start": 1610,
"cdna_end": null,
"cdna_length": 4395,
"mane_select": "NM_025132.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_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": "c.1101C>A",
"hgvs_p": "p.Thr367Thr",
"transcript": "NM_001317924.2",
"protein_id": "NP_001304853.1",
"transcript_support_level": null,
"aa_start": 367,
"aa_end": null,
"aa_length": 1182,
"cds_start": 1101,
"cds_end": null,
"cds_length": 3549,
"cdna_start": 1494,
"cdna_end": null,
"cdna_length": 4279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"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.1581C>A",
"hgvs_p": "p.Thr527Thr",
"transcript": "XM_011513724.2",
"protein_id": "XP_011512026.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1346,
"cds_start": 1581,
"cds_end": null,
"cds_length": 4041,
"cdna_start": 1610,
"cdna_end": null,
"cdna_length": 4407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_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": "c.1515C>A",
"hgvs_p": "p.Thr505Thr",
"transcript": "XM_011513725.3",
"protein_id": "XP_011512027.1",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 1324,
"cds_start": 1515,
"cds_end": null,
"cds_length": 3975,
"cdna_start": 1544,
"cdna_end": null,
"cdna_length": 4341,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_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": "c.1515C>A",
"hgvs_p": "p.Thr505Thr",
"transcript": "XM_047416030.1",
"protein_id": "XP_047271986.1",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 1320,
"cds_start": 1515,
"cds_end": null,
"cds_length": 3963,
"cdna_start": 1544,
"cdna_end": null,
"cdna_length": 4329,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"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.1581C>A",
"hgvs_p": "p.Thr527Thr",
"transcript": "XM_047416031.1",
"protein_id": "XP_047271987.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1195,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3588,
"cdna_start": 1610,
"cdna_end": null,
"cdna_length": 5387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"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.1581C>A",
"hgvs_p": "p.Thr527Thr",
"transcript": "XM_047416032.1",
"protein_id": "XP_047271988.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1191,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3576,
"cdna_start": 1610,
"cdna_end": null,
"cdna_length": 5375,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"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.1101C>A",
"hgvs_p": "p.Thr367Thr",
"transcript": "XM_047416033.1",
"protein_id": "XP_047271989.1",
"transcript_support_level": null,
"aa_start": 367,
"aa_end": null,
"aa_length": 1186,
"cds_start": 1101,
"cds_end": null,
"cds_length": 3561,
"cdna_start": 1264,
"cdna_end": null,
"cdna_length": 4061,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"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.1581C>A",
"hgvs_p": "p.Thr527Thr",
"transcript": "XM_047416034.1",
"protein_id": "XP_047271990.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 969,
"cds_start": 1581,
"cds_end": null,
"cds_length": 2910,
"cdna_start": 1610,
"cdna_end": null,
"cdna_length": 2978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"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.1581C>A",
"hgvs_p": "p.Thr527Thr",
"transcript": "XM_047416035.1",
"protein_id": "XP_047271991.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 761,
"cds_start": 1581,
"cds_end": null,
"cds_length": 2286,
"cdna_start": 1610,
"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.*1162C>A",
"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.579C>A",
"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.*1162C>A",
"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.41-3573C>A",
"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": "rs114689848",
"frequency_reference_population": 0.0015379512,
"hom_count_reference_population": 37,
"allele_count_reference_population": 2420,
"gnomad_exomes_af": 0.0008103,
"gnomad_genomes_af": 0.00835167,
"gnomad_exomes_ac": 1152,
"gnomad_genomes_ac": 1268,
"gnomad_exomes_homalt": 20,
"gnomad_genomes_homalt": 17,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.25999999046325684,
"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": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.708,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000399820.8",
"gene_symbol": "WDR19",
"hgnc_id": 18340,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1581C>A",
"hgvs_p": "p.Thr527Thr"
}
],
"clinvar_disease": "Asphyxiating thoracic dystrophy 5,Connective tissue disorder,Cranioectodermal dysplasia 4,Nephronophthisis 13,Senior-Loken syndrome 8,Spermatogenic failure 72,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:11",
"phenotype_combined": "not specified|Senior-Loken syndrome 8;Asphyxiating thoracic dystrophy 5|Asphyxiating thoracic dystrophy 5|Cranioectodermal dysplasia 4|Connective tissue disorder|Spermatogenic failure 72;Senior-Loken syndrome 8;Asphyxiating thoracic dystrophy 5;Nephronophthisis 13;Cranioectodermal dysplasia 4|not provided|Senior-Loken syndrome 8|Nephronophthisis 13",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}