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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: 17-3656529-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=3656529&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 3656529,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000046640.9",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Thr168Thr",
"transcript": "NM_004937.3",
"protein_id": "NP_004928.2",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 367,
"cds_start": 504,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 805,
"cdna_end": null,
"cdna_length": 4139,
"mane_select": "ENST00000046640.9",
"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": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Thr168Thr",
"transcript": "ENST00000046640.9",
"protein_id": "ENSP00000046640.4",
"transcript_support_level": 1,
"aa_start": 168,
"aa_end": null,
"aa_length": 367,
"cds_start": 504,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 805,
"cdna_end": null,
"cdna_length": 4139,
"mane_select": "NM_004937.3",
"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": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Thr168Thr",
"transcript": "ENST00000381870.8",
"protein_id": "ENSP00000371294.3",
"transcript_support_level": 1,
"aa_start": 168,
"aa_end": null,
"aa_length": 400,
"cds_start": 504,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 983,
"cdna_end": null,
"cdna_length": 2490,
"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": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Thr168Thr",
"transcript": "NM_001031681.3",
"protein_id": "NP_001026851.2",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 400,
"cds_start": 504,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 983,
"cdna_end": null,
"cdna_length": 4051,
"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": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Thr168Thr",
"transcript": "NM_001374492.1",
"protein_id": "NP_001361421.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 400,
"cds_start": 504,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 805,
"cdna_end": null,
"cdna_length": 3873,
"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": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Thr168Thr",
"transcript": "ENST00000673965.1",
"protein_id": "ENSP00000500995.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 367,
"cds_start": 504,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 978,
"cdna_end": null,
"cdna_length": 2657,
"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": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Thr21Thr",
"transcript": "ENST00000574776.6",
"protein_id": "ENSP00000461118.2",
"transcript_support_level": 4,
"aa_start": 21,
"aa_end": null,
"aa_length": 253,
"cds_start": 63,
"cds_end": null,
"cds_length": 762,
"cdna_start": 568,
"cdna_end": null,
"cdna_length": 1570,
"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": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Thr21Thr",
"transcript": "NM_001374493.1",
"protein_id": "NP_001361422.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 220,
"cds_start": 63,
"cds_end": null,
"cds_length": 663,
"cdna_start": 720,
"cdna_end": null,
"cdna_length": 4054,
"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": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Thr21Thr",
"transcript": "NM_001374494.1",
"protein_id": "NP_001361423.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 220,
"cds_start": 63,
"cds_end": null,
"cds_length": 663,
"cdna_start": 725,
"cdna_end": null,
"cdna_length": 4059,
"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": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Thr21Thr",
"transcript": "NM_001374495.1",
"protein_id": "NP_001361424.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 220,
"cds_start": 63,
"cds_end": null,
"cds_length": 663,
"cdna_start": 641,
"cdna_end": null,
"cdna_length": 3975,
"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": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Thr21Thr",
"transcript": "NM_001374496.1",
"protein_id": "NP_001361425.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 220,
"cds_start": 63,
"cds_end": null,
"cds_length": 663,
"cdna_start": 640,
"cdna_end": null,
"cdna_length": 3974,
"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": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Thr21Thr",
"transcript": "ENST00000673669.1",
"protein_id": "ENSP00000501123.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 220,
"cds_start": 63,
"cds_end": null,
"cds_length": 663,
"cdna_start": 674,
"cdna_end": null,
"cdna_length": 2417,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Thr21Thr",
"transcript": "ENST00000574218.1",
"protein_id": "ENSP00000458912.1",
"transcript_support_level": 5,
"aa_start": 21,
"aa_end": null,
"aa_length": 27,
"cds_start": 63,
"cds_end": null,
"cds_length": 85,
"cdna_start": 559,
"cdna_end": null,
"cdna_length": 581,
"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": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Thr168Thr",
"transcript": "XM_006721463.4",
"protein_id": "XP_006721526.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 400,
"cds_start": 504,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 978,
"cdna_end": null,
"cdna_length": 4046,
"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": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Thr168Thr",
"transcript": "XM_011523691.3",
"protein_id": "XP_011521993.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 400,
"cds_start": 504,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 861,
"cdna_end": null,
"cdna_length": 3929,
"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": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Thr168Thr",
"transcript": "XM_047435501.1",
"protein_id": "XP_047291457.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 298,
"cds_start": 504,
"cds_end": null,
"cds_length": 897,
"cdna_start": 805,
"cdna_end": null,
"cdna_length": 2825,
"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": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Thr21Thr",
"transcript": "XM_011523692.3",
"protein_id": "XP_011521994.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 253,
"cds_start": 63,
"cds_end": null,
"cds_length": 762,
"cdna_start": 725,
"cdna_end": null,
"cdna_length": 3793,
"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": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "n.805G>A",
"hgvs_p": null,
"transcript": "XR_007065277.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.-250G>A",
"hgvs_p": null,
"transcript": "ENST00000488623.6",
"protein_id": "ENSP00000501016.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 116,
"cds_start": -4,
"cds_end": null,
"cds_length": 351,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2322,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CTNS-AS1",
"gene_hgnc_id": 56090,
"hgvs_c": "n.532+327C>T",
"hgvs_p": null,
"transcript": "ENST00000575741.1",
"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": 874,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.*16G>A",
"hgvs_p": null,
"transcript": "ENST00000576979.1",
"protein_id": "ENSP00000458457.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 161,
"cds_start": -4,
"cds_end": null,
"cds_length": 488,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"dbsnp": "rs1800528",
"frequency_reference_population": 0.1842842,
"hom_count_reference_population": 28811,
"allele_count_reference_population": 295569,
"gnomad_exomes_af": 0.187543,
"gnomad_genomes_af": 0.150956,
"gnomad_exomes_ac": 274004,
"gnomad_genomes_ac": 21565,
"gnomad_exomes_homalt": 26763,
"gnomad_genomes_homalt": 2048,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6499999761581421,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.65,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.823,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000046640.9",
"gene_symbol": "CTNS",
"hgnc_id": 2518,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Thr168Thr"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000575741.1",
"gene_symbol": "CTNS-AS1",
"hgnc_id": 56090,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.532+327C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Cystinosis,Inborn genetic diseases,Juvenile nephropathic cystinosis,Nephropathic cystinosis,Ocular cystinosis,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:10",
"phenotype_combined": "not specified|Nephropathic cystinosis|Ocular cystinosis|not provided|Ocular cystinosis;Juvenile nephropathic cystinosis;Inborn genetic diseases|Cystinosis",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}