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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: 11-1757389-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=1757389&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 1757389,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000236671.7",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.639C>T",
"hgvs_p": "p.Pro213Pro",
"transcript": "NM_001909.5",
"protein_id": "NP_001900.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 412,
"cds_start": 639,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 707,
"cdna_end": null,
"cdna_length": 2055,
"mane_select": "ENST00000236671.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.639C>T",
"hgvs_p": "p.Pro213Pro",
"transcript": "ENST00000236671.7",
"protein_id": "ENSP00000236671.2",
"transcript_support_level": 1,
"aa_start": 213,
"aa_end": null,
"aa_length": 412,
"cds_start": 639,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 707,
"cdna_end": null,
"cdna_length": 2055,
"mane_select": "NM_001909.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250644",
"gene_hgnc_id": null,
"hgvs_c": "c.639C>T",
"hgvs_p": "p.Pro213Pro",
"transcript": "ENST00000636615.1",
"protein_id": "ENSP00000490014.1",
"transcript_support_level": 5,
"aa_start": 213,
"aa_end": null,
"aa_length": 557,
"cds_start": 639,
"cds_end": null,
"cds_length": 1674,
"cdna_start": 734,
"cdna_end": null,
"cdna_length": 2228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250644",
"gene_hgnc_id": null,
"hgvs_c": "c.639C>T",
"hgvs_p": "p.Pro213Pro",
"transcript": "ENST00000636397.1",
"protein_id": "ENSP00000489910.1",
"transcript_support_level": 5,
"aa_start": 213,
"aa_end": null,
"aa_length": 582,
"cds_start": 639,
"cds_end": null,
"cds_length": 1749,
"cdna_start": 712,
"cdna_end": null,
"cdna_length": 4038,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.639C>T",
"hgvs_p": "p.Pro213Pro",
"transcript": "ENST00000438213.6",
"protein_id": "ENSP00000415036.2",
"transcript_support_level": 2,
"aa_start": 213,
"aa_end": null,
"aa_length": 451,
"cds_start": 639,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 707,
"cdna_end": null,
"cdna_length": 1544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.633C>T",
"hgvs_p": "p.Pro211Pro",
"transcript": "ENST00000636843.1",
"protein_id": "ENSP00000490897.1",
"transcript_support_level": 5,
"aa_start": 211,
"aa_end": null,
"aa_length": 410,
"cds_start": 633,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 722,
"cdna_end": null,
"cdna_length": 1512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.639C>T",
"hgvs_p": "p.Pro213Pro",
"transcript": "ENST00000637915.1",
"protein_id": "ENSP00000490471.1",
"transcript_support_level": 5,
"aa_start": 213,
"aa_end": null,
"aa_length": 409,
"cds_start": 639,
"cds_end": null,
"cds_length": 1230,
"cdna_start": 676,
"cdna_end": null,
"cdna_length": 1982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.639C>T",
"hgvs_p": "p.Pro213Pro",
"transcript": "ENST00000637815.2",
"protein_id": "ENSP00000490344.1",
"transcript_support_level": 5,
"aa_start": 213,
"aa_end": null,
"aa_length": 406,
"cds_start": 639,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 686,
"cdna_end": null,
"cdna_length": 2019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.618C>T",
"hgvs_p": "p.Pro206Pro",
"transcript": "ENST00000636571.1",
"protein_id": "ENSP00000490770.1",
"transcript_support_level": 5,
"aa_start": 206,
"aa_end": null,
"aa_length": 405,
"cds_start": 618,
"cds_end": null,
"cds_length": 1218,
"cdna_start": 686,
"cdna_end": null,
"cdna_length": 1790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.639C>T",
"hgvs_p": "p.Pro213Pro",
"transcript": "ENST00000637387.1",
"protein_id": "ENSP00000490598.1",
"transcript_support_level": 5,
"aa_start": 213,
"aa_end": null,
"aa_length": 405,
"cds_start": 639,
"cds_end": null,
"cds_length": 1218,
"cdna_start": 721,
"cdna_end": null,
"cdna_length": 1597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.534C>T",
"hgvs_p": "p.Pro178Pro",
"transcript": "ENST00000367196.4",
"protein_id": "ENSP00000356164.4",
"transcript_support_level": 5,
"aa_start": 178,
"aa_end": null,
"aa_length": 377,
"cds_start": 534,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 842,
"cdna_end": null,
"cdna_length": 2190,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.534C>T",
"hgvs_p": "p.Pro178Pro",
"transcript": "ENST00000429746.2",
"protein_id": "ENSP00000402586.2",
"transcript_support_level": 3,
"aa_start": 178,
"aa_end": null,
"aa_length": 377,
"cds_start": 534,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 625,
"cdna_end": null,
"cdna_length": 1973,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250644",
"gene_hgnc_id": null,
"hgvs_c": "c.63C>T",
"hgvs_p": "p.Pro21Pro",
"transcript": "ENST00000427721.3",
"protein_id": "ENSP00000415840.3",
"transcript_support_level": 2,
"aa_start": 21,
"aa_end": null,
"aa_length": 334,
"cds_start": 63,
"cds_end": null,
"cds_length": 1006,
"cdna_start": 64,
"cdna_end": null,
"cdna_length": 1007,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.639C>T",
"hgvs_p": null,
"transcript": "ENST00000433655.6",
"protein_id": "ENSP00000404902.1",
"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": 2035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.237C>T",
"hgvs_p": null,
"transcript": "ENST00000637158.1",
"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": 1200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.3067C>T",
"hgvs_p": null,
"transcript": "ENST00000637381.2",
"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": 4408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.1034C>T",
"hgvs_p": null,
"transcript": "ENST00000677300.1",
"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": 1081,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.*500C>T",
"hgvs_p": null,
"transcript": "ENST00000678991.1",
"protein_id": "ENSP00000503019.1",
"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": 2198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.*500C>T",
"hgvs_p": null,
"transcript": "ENST00000678991.1",
"protein_id": "ENSP00000503019.1",
"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": 2198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"dbsnp": "rs146073498",
"frequency_reference_population": 0.000027260516,
"hom_count_reference_population": 0,
"allele_count_reference_population": 44,
"gnomad_exomes_af": 0.0000266797,
"gnomad_genomes_af": 0.000032836,
"gnomad_exomes_ac": 39,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.32499998807907104,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.325,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.363,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Moderate,BP7,BS1",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000236671.7",
"gene_symbol": "CTSD",
"hgnc_id": 2529,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.639C>T",
"hgvs_p": "p.Pro213Pro"
},
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000636615.1",
"gene_symbol": "ENSG00000250644",
"hgnc_id": null,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.639C>T",
"hgvs_p": "p.Pro213Pro"
}
],
"clinvar_disease": "CTSD-related disorder,Neuronal ceroid lipofuscinosis",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "CTSD-related disorder|Neuronal ceroid lipofuscinosis",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}