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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: 17-3656498-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=3656498&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 3656498,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000046640.9",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.473T>C",
"hgvs_p": "p.Leu158Pro",
"transcript": "NM_004937.3",
"protein_id": "NP_004928.2",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 367,
"cds_start": 473,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 774,
"cdna_end": null,
"cdna_length": 4139,
"mane_select": "ENST00000046640.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.473T>C",
"hgvs_p": "p.Leu158Pro",
"transcript": "ENST00000046640.9",
"protein_id": "ENSP00000046640.4",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 367,
"cds_start": 473,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 774,
"cdna_end": null,
"cdna_length": 4139,
"mane_select": "NM_004937.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.473T>C",
"hgvs_p": "p.Leu158Pro",
"transcript": "ENST00000381870.8",
"protein_id": "ENSP00000371294.3",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 400,
"cds_start": 473,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 952,
"cdna_end": null,
"cdna_length": 2490,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.473T>C",
"hgvs_p": "p.Leu158Pro",
"transcript": "NM_001031681.3",
"protein_id": "NP_001026851.2",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 400,
"cds_start": 473,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 952,
"cdna_end": null,
"cdna_length": 4051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.473T>C",
"hgvs_p": "p.Leu158Pro",
"transcript": "NM_001374492.1",
"protein_id": "NP_001361421.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 400,
"cds_start": 473,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 774,
"cdna_end": null,
"cdna_length": 3873,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.473T>C",
"hgvs_p": "p.Leu158Pro",
"transcript": "ENST00000673965.1",
"protein_id": "ENSP00000500995.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 367,
"cds_start": 473,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 947,
"cdna_end": null,
"cdna_length": 2657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.32T>C",
"hgvs_p": "p.Leu11Pro",
"transcript": "ENST00000574776.6",
"protein_id": "ENSP00000461118.2",
"transcript_support_level": 4,
"aa_start": 11,
"aa_end": null,
"aa_length": 253,
"cds_start": 32,
"cds_end": null,
"cds_length": 762,
"cdna_start": 537,
"cdna_end": null,
"cdna_length": 1570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.32T>C",
"hgvs_p": "p.Leu11Pro",
"transcript": "NM_001374493.1",
"protein_id": "NP_001361422.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 220,
"cds_start": 32,
"cds_end": null,
"cds_length": 663,
"cdna_start": 689,
"cdna_end": null,
"cdna_length": 4054,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.32T>C",
"hgvs_p": "p.Leu11Pro",
"transcript": "NM_001374494.1",
"protein_id": "NP_001361423.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 220,
"cds_start": 32,
"cds_end": null,
"cds_length": 663,
"cdna_start": 694,
"cdna_end": null,
"cdna_length": 4059,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.32T>C",
"hgvs_p": "p.Leu11Pro",
"transcript": "NM_001374495.1",
"protein_id": "NP_001361424.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 220,
"cds_start": 32,
"cds_end": null,
"cds_length": 663,
"cdna_start": 610,
"cdna_end": null,
"cdna_length": 3975,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.32T>C",
"hgvs_p": "p.Leu11Pro",
"transcript": "NM_001374496.1",
"protein_id": "NP_001361425.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 220,
"cds_start": 32,
"cds_end": null,
"cds_length": 663,
"cdna_start": 609,
"cdna_end": null,
"cdna_length": 3974,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.32T>C",
"hgvs_p": "p.Leu11Pro",
"transcript": "ENST00000673669.1",
"protein_id": "ENSP00000501123.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 220,
"cds_start": 32,
"cds_end": null,
"cds_length": 663,
"cdna_start": 643,
"cdna_end": null,
"cdna_length": 2417,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"hgvs_c": "c.473T>C",
"hgvs_p": "p.Leu158Pro",
"transcript": "ENST00000576979.1",
"protein_id": "ENSP00000458457.1",
"transcript_support_level": 5,
"aa_start": 158,
"aa_end": null,
"aa_length": 161,
"cds_start": 473,
"cds_end": null,
"cds_length": 488,
"cdna_start": 533,
"cdna_end": null,
"cdna_length": 548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.32T>C",
"hgvs_p": "p.Leu11Pro",
"transcript": "ENST00000574218.1",
"protein_id": "ENSP00000458912.1",
"transcript_support_level": 5,
"aa_start": 11,
"aa_end": null,
"aa_length": 27,
"cds_start": 32,
"cds_end": null,
"cds_length": 85,
"cdna_start": 528,
"cdna_end": null,
"cdna_length": 581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.473T>C",
"hgvs_p": "p.Leu158Pro",
"transcript": "XM_006721463.4",
"protein_id": "XP_006721526.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 400,
"cds_start": 473,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 947,
"cdna_end": null,
"cdna_length": 4046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.473T>C",
"hgvs_p": "p.Leu158Pro",
"transcript": "XM_011523691.3",
"protein_id": "XP_011521993.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 400,
"cds_start": 473,
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"cds_length": 1203,
"cdna_start": 830,
"cdna_end": null,
"cdna_length": 3929,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.473T>C",
"hgvs_p": "p.Leu158Pro",
"transcript": "XM_047435501.1",
"protein_id": "XP_047291457.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 298,
"cds_start": 473,
"cds_end": null,
"cds_length": 897,
"cdna_start": 774,
"cdna_end": null,
"cdna_length": 2825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.32T>C",
"hgvs_p": "p.Leu11Pro",
"transcript": "XM_011523692.3",
"protein_id": "XP_011521994.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 253,
"cds_start": 32,
"cds_end": null,
"cds_length": 762,
"cdna_start": 694,
"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.774T>C",
"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.-281T>C",
"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+358A>G",
"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
}
],
"gene_symbol": "CTNS",
"gene_hgnc_id": 2518,
"dbsnp": "rs113994206",
"frequency_reference_population": 0.00011138631,
"hom_count_reference_population": 0,
"allele_count_reference_population": 178,
"gnomad_exomes_af": 0.000117802,
"gnomad_genomes_af": 0.0000434909,
"gnomad_exomes_ac": 172,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9571309685707092,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.987,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9861,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.57,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.987,
"phylop100way_prediction": "Uncertain_significance",
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000046640.9",
"gene_symbol": "CTNS",
"hgnc_id": 2518,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.473T>C",
"hgvs_p": "p.Leu158Pro"
},
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000575741.1",
"gene_symbol": "CTNS-AS1",
"hgnc_id": 56090,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.532+358A>G",
"hgvs_p": null
}
],
"clinvar_disease": "CTNS-related disorder,Cystinosis,Inborn genetic diseases,Juvenile nephropathic cystinosis,Nephropathic cystinosis,Ocular cystinosis,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 LP:2 O:1",
"phenotype_combined": "Nephropathic cystinosis|not provided|Ocular cystinosis;Juvenile nephropathic cystinosis;Inborn genetic diseases|Ocular cystinosis;Juvenile nephropathic cystinosis;Nephropathic cystinosis|CTNS-related disorder|Cystinosis",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}