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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: 4-39244470-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=39244470&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP3",
"PP5"
],
"effects": [
"stop_gained",
"splice_region_variant"
],
"gene_symbol": "WDR19",
"hgnc_id": 18340,
"hgvs_c": "c.2563C>T",
"hgvs_p": "p.Gln855*",
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_025132.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP3,PP5",
"acmg_score": 12,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.66,
"chr": "4",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Jeune thoracic dystrophy",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6600000262260437,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1342,
"aa_ref": "Q",
"aa_start": 855,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4395,
"cdna_start": 2592,
"cds_end": null,
"cds_length": 4029,
"cds_start": 2563,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 37,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "NM_025132.4",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2563C>T",
"hgvs_p": "p.Gln855*",
"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": "*",
"aa_end": null,
"aa_length": 1342,
"aa_ref": "Q",
"aa_start": 855,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4395,
"cdna_start": 2592,
"cds_end": null,
"cds_length": 4029,
"cds_start": 2563,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 37,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000399820.8",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2563C>T",
"hgvs_p": "p.Gln855*",
"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": "*",
"aa_end": null,
"aa_length": 1346,
"aa_ref": "Q",
"aa_start": 859,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4429,
"cdna_start": 2627,
"cds_end": null,
"cds_length": 4041,
"cds_start": 2575,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 37,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000959578.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2575C>T",
"hgvs_p": "p.Gln859*",
"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": "*",
"aa_end": null,
"aa_length": 1320,
"aa_ref": "Q",
"aa_start": 833,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4364,
"cdna_start": 2561,
"cds_end": null,
"cds_length": 3963,
"cds_start": 2497,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 36,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000919861.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2497C>T",
"hgvs_p": "p.Gln833*",
"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": "*",
"aa_end": null,
"aa_length": 1319,
"aa_ref": "Q",
"aa_start": 833,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4323,
"cdna_start": 2524,
"cds_end": null,
"cds_length": 3960,
"cds_start": 2497,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 36,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000867847.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2497C>T",
"hgvs_p": "p.Gln833*",
"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": "*",
"aa_end": null,
"aa_length": 1316,
"aa_ref": "Q",
"aa_start": 855,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4323,
"cdna_start": 2602,
"cds_end": null,
"cds_length": 3951,
"cds_start": 2563,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 36,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000867846.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2563C>T",
"hgvs_p": "p.Gln855*",
"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": "*",
"aa_end": null,
"aa_length": 1182,
"aa_ref": "Q",
"aa_start": 695,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4279,
"cdna_start": 2476,
"cds_end": null,
"cds_length": 3549,
"cds_start": 2083,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 36,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "NM_001317924.2",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2083C>T",
"hgvs_p": "p.Gln695*",
"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": "*",
"aa_end": null,
"aa_length": 1346,
"aa_ref": "Q",
"aa_start": 859,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4407,
"cdna_start": 2604,
"cds_end": null,
"cds_length": 4041,
"cds_start": 2575,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 37,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_011513724.2",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2575C>T",
"hgvs_p": "p.Gln859*",
"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": "*",
"aa_end": null,
"aa_length": 1324,
"aa_ref": "Q",
"aa_start": 837,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4341,
"cdna_start": 2538,
"cds_end": null,
"cds_length": 3975,
"cds_start": 2509,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 36,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_011513725.3",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2509C>T",
"hgvs_p": "p.Gln837*",
"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": "*",
"aa_end": null,
"aa_length": 1320,
"aa_ref": "Q",
"aa_start": 833,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4329,
"cdna_start": 2526,
"cds_end": null,
"cds_length": 3963,
"cds_start": 2497,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 36,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_047416030.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2497C>T",
"hgvs_p": "p.Gln833*",
"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": "*",
"aa_end": null,
"aa_length": 1195,
"aa_ref": "Q",
"aa_start": 859,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5387,
"cdna_start": 2604,
"cds_end": null,
"cds_length": 3588,
"cds_start": 2575,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 33,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_047416031.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2575C>T",
"hgvs_p": "p.Gln859*",
"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": "*",
"aa_end": null,
"aa_length": 1191,
"aa_ref": "Q",
"aa_start": 855,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5375,
"cdna_start": 2592,
"cds_end": null,
"cds_length": 3576,
"cds_start": 2563,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 33,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_047416032.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2563C>T",
"hgvs_p": "p.Gln855*",
"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": "*",
"aa_end": null,
"aa_length": 1186,
"aa_ref": "Q",
"aa_start": 699,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4061,
"cdna_start": 2258,
"cds_end": null,
"cds_length": 3561,
"cds_start": 2095,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 33,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047416033.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2095C>T",
"hgvs_p": "p.Gln699*",
"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": "*",
"aa_end": null,
"aa_length": 969,
"aa_ref": "Q",
"aa_start": 859,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2978,
"cdna_start": 2604,
"cds_end": null,
"cds_length": 2910,
"cds_start": 2575,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 26,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_047416034.1",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "c.2575C>T",
"hgvs_p": "p.Gln859*",
"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": 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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 36,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000506869.5",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "n.*2144C>T",
"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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000512095.5",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "n.1561C>T",
"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": 22,
"exon_rank_end": null,
"feature": "ENST00000506869.5",
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"hgvs_c": "n.*2144C>T",
"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
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.996331783378635,
"dbsnp": "rs772599282",
"effect": "stop_gained,splice_region_variant",
"frequency_reference_population": 0.0000013683073,
"gene_hgnc_id": 18340,
"gene_symbol": "WDR19",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000136831,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Jeune thoracic dystrophy",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.841,
"pos": 39244470,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9120000004768372,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.12,
"transcript": "NM_025132.4"
}
]
}