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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: 4-39225011-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=39225011&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "WDR19",
"hgnc_id": 18340,
"hgvs_c": "c.1607G>C",
"hgvs_p": "p.Ser536Thr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_025132.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 2400,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0941,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.14,
"chr": "4",
"clinvar_classification": "Benign",
"clinvar_disease": "Asphyxiating thoracic dystrophy 5,Connective tissue disorder,Cranioectodermal dysplasia 4,Nephronophthisis 13,Senior-Loken syndrome 8,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:11",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.007390111684799194,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1342,
"aa_ref": "S",
"aa_start": 536,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4395,
"cdna_start": 1636,
"cds_end": null,
"cds_length": 4029,
"cds_start": 1607,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_025132.4",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1607G>C",
"hgvs_p": "p.Ser536Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000399820.8",
"protein_coding": true,
"protein_id": "NP_079408.3",
"strand": true,
"transcript": "NM_025132.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1342,
"aa_ref": "S",
"aa_start": 536,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4395,
"cdna_start": 1636,
"cds_end": null,
"cds_length": 4029,
"cds_start": 1607,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000399820.8",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1607G>C",
"hgvs_p": "p.Ser536Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_025132.4",
"protein_coding": true,
"protein_id": "ENSP00000382717.3",
"strand": true,
"transcript": "ENST00000399820.8",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1346,
"aa_ref": "S",
"aa_start": 536,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4429,
"cdna_start": 1659,
"cds_end": null,
"cds_length": 4041,
"cds_start": 1607,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000959578.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1607G>C",
"hgvs_p": "p.Ser536Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629637.1",
"strand": true,
"transcript": "ENST00000959578.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1320,
"aa_ref": "S",
"aa_start": 514,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4364,
"cdna_start": 1605,
"cds_end": null,
"cds_length": 3963,
"cds_start": 1541,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000919861.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1541G>C",
"hgvs_p": "p.Ser514Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589920.1",
"strand": true,
"transcript": "ENST00000919861.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1319,
"aa_ref": "S",
"aa_start": 514,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4323,
"cdna_start": 1568,
"cds_end": null,
"cds_length": 3960,
"cds_start": 1541,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000867847.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1541G>C",
"hgvs_p": "p.Ser514Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537906.1",
"strand": true,
"transcript": "ENST00000867847.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1316,
"aa_ref": "S",
"aa_start": 536,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4323,
"cdna_start": 1646,
"cds_end": null,
"cds_length": 3951,
"cds_start": 1607,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000867846.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1607G>C",
"hgvs_p": "p.Ser536Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537905.1",
"strand": true,
"transcript": "ENST00000867846.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1182,
"aa_ref": "S",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4279,
"cdna_start": 1520,
"cds_end": null,
"cds_length": 3549,
"cds_start": 1127,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_001317924.2",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1127G>C",
"hgvs_p": "p.Ser376Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001304853.1",
"strand": true,
"transcript": "NM_001317924.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1346,
"aa_ref": "S",
"aa_start": 536,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4407,
"cdna_start": 1636,
"cds_end": null,
"cds_length": 4041,
"cds_start": 1607,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_011513724.2",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1607G>C",
"hgvs_p": "p.Ser536Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512026.1",
"strand": true,
"transcript": "XM_011513724.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1324,
"aa_ref": "S",
"aa_start": 514,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4341,
"cdna_start": 1570,
"cds_end": null,
"cds_length": 3975,
"cds_start": 1541,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_011513725.3",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1541G>C",
"hgvs_p": "p.Ser514Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512027.1",
"strand": true,
"transcript": "XM_011513725.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1320,
"aa_ref": "S",
"aa_start": 514,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4329,
"cdna_start": 1570,
"cds_end": null,
"cds_length": 3963,
"cds_start": 1541,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_047416030.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1541G>C",
"hgvs_p": "p.Ser514Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271986.1",
"strand": true,
"transcript": "XM_047416030.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1195,
"aa_ref": "S",
"aa_start": 536,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5387,
"cdna_start": 1636,
"cds_end": null,
"cds_length": 3588,
"cds_start": 1607,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_047416031.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1607G>C",
"hgvs_p": "p.Ser536Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271987.1",
"strand": true,
"transcript": "XM_047416031.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1191,
"aa_ref": "S",
"aa_start": 536,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5375,
"cdna_start": 1636,
"cds_end": null,
"cds_length": 3576,
"cds_start": 1607,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_047416032.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1607G>C",
"hgvs_p": "p.Ser536Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271988.1",
"strand": true,
"transcript": "XM_047416032.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1186,
"aa_ref": "S",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4061,
"cdna_start": 1290,
"cds_end": null,
"cds_length": 3561,
"cds_start": 1127,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_047416033.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1127G>C",
"hgvs_p": "p.Ser376Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271989.1",
"strand": true,
"transcript": "XM_047416033.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 969,
"aa_ref": "S",
"aa_start": 536,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2978,
"cdna_start": 1636,
"cds_end": null,
"cds_length": 2910,
"cds_start": 1607,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_047416034.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1607G>C",
"hgvs_p": "p.Ser536Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271990.1",
"strand": true,
"transcript": "XM_047416034.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 761,
"aa_ref": "S",
"aa_start": 536,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2377,
"cdna_start": 1636,
"cds_end": null,
"cds_length": 2286,
"cds_start": 1607,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_047416035.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.1607G>C",
"hgvs_p": "p.Ser536Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271991.1",
"strand": true,
"transcript": "XM_047416035.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4249,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 36,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000506869.5",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "n.*1188G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000424319.1",
"strand": true,
"transcript": "ENST00000506869.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3095,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000512095.5",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "n.605G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000512095.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4249,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 36,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000506869.5",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "n.*1188G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000424319.1",
"strand": true,
"transcript": "ENST00000506869.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 510,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000511729.5",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "n.41-3547G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000511729.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs115348383",
"effect": "missense_variant",
"frequency_reference_population": 0.001533317,
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"gnomad_exomes_ac": 1127,
"gnomad_exomes_af": 0.000797532,
"gnomad_exomes_homalt": 21,
"gnomad_genomes_ac": 1273,
"gnomad_genomes_af": 0.00836817,
"gnomad_genomes_homalt": 17,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 38,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Senior-Loken syndrome 8;Asphyxiating thoracic dystrophy 5|Asphyxiating thoracic dystrophy 5|not provided|Cranioectodermal dysplasia 4|Connective tissue disorder|Senior-Loken syndrome 8|Nephronophthisis 13",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.627,
"pos": 39225011,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.416,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_025132.4"
}
]
}