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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: 12-122232917-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=122232917&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 122232917,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000267199.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "c.1492C>T",
"hgvs_p": "p.Arg498Trp",
"transcript": "NM_022916.6",
"protein_id": "NP_075067.2",
"transcript_support_level": null,
"aa_start": 498,
"aa_end": null,
"aa_length": 596,
"cds_start": 1492,
"cds_end": null,
"cds_length": 1791,
"cdna_start": 1578,
"cdna_end": null,
"cdna_length": 4559,
"mane_select": "ENST00000267199.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "c.1492C>T",
"hgvs_p": "p.Arg498Trp",
"transcript": "ENST00000267199.9",
"protein_id": "ENSP00000267199.3",
"transcript_support_level": 1,
"aa_start": 498,
"aa_end": null,
"aa_length": 596,
"cds_start": 1492,
"cds_end": null,
"cds_length": 1791,
"cdna_start": 1578,
"cdna_end": null,
"cdna_length": 4559,
"mane_select": "NM_022916.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000256861",
"gene_hgnc_id": null,
"hgvs_c": "n.1375C>T",
"hgvs_p": null,
"transcript": "ENST00000535844.1",
"protein_id": "ENSP00000454454.1",
"transcript_support_level": 2,
"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": 2748,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "c.1639C>T",
"hgvs_p": "p.Arg547Trp",
"transcript": "ENST00000536212.3",
"protein_id": "ENSP00000439255.3",
"transcript_support_level": 4,
"aa_start": 547,
"aa_end": null,
"aa_length": 645,
"cds_start": 1639,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 1664,
"cdna_end": null,
"cdna_length": 2323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "c.1615C>T",
"hgvs_p": "p.Arg539Trp",
"transcript": "ENST00000643696.1",
"protein_id": "ENSP00000494935.1",
"transcript_support_level": null,
"aa_start": 539,
"aa_end": null,
"aa_length": 637,
"cds_start": 1615,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 1640,
"cdna_end": null,
"cdna_length": 2299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Arg491Trp",
"transcript": "ENST00000714045.1",
"protein_id": "ENSP00000519336.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 589,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1770,
"cdna_start": 1545,
"cdna_end": null,
"cdna_length": 4511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "c.1459C>T",
"hgvs_p": "p.Arg487Trp",
"transcript": "NM_001351018.2",
"protein_id": "NP_001337947.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 585,
"cds_start": 1459,
"cds_end": null,
"cds_length": 1758,
"cdna_start": 1808,
"cdna_end": null,
"cdna_length": 4789,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "c.1444C>T",
"hgvs_p": "p.Arg482Trp",
"transcript": "NM_001351019.2",
"protein_id": "NP_001337948.1",
"transcript_support_level": null,
"aa_start": 482,
"aa_end": null,
"aa_length": 580,
"cds_start": 1444,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1890,
"cdna_end": null,
"cdna_length": 4871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "c.1306C>T",
"hgvs_p": "p.Arg436Trp",
"transcript": "ENST00000714042.1",
"protein_id": "ENSP00000519333.1",
"transcript_support_level": null,
"aa_start": 436,
"aa_end": null,
"aa_length": 534,
"cds_start": 1306,
"cds_end": null,
"cds_length": 1605,
"cdna_start": 1638,
"cdna_end": null,
"cdna_length": 4614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "c.1306C>T",
"hgvs_p": "p.Arg436Trp",
"transcript": "ENST00000714043.1",
"protein_id": "ENSP00000519334.1",
"transcript_support_level": null,
"aa_start": 436,
"aa_end": null,
"aa_length": 534,
"cds_start": 1306,
"cds_end": null,
"cds_length": 1605,
"cdna_start": 1714,
"cdna_end": null,
"cdna_length": 4685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "c.1171C>T",
"hgvs_p": "p.Arg391Trp",
"transcript": "NM_001351020.2",
"protein_id": "NP_001337949.1",
"transcript_support_level": null,
"aa_start": 391,
"aa_end": null,
"aa_length": 489,
"cds_start": 1171,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 1257,
"cdna_end": null,
"cdna_length": 4238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "c.1033C>T",
"hgvs_p": "p.Arg345Trp",
"transcript": "ENST00000541169.2",
"protein_id": "ENSP00000495062.2",
"transcript_support_level": 4,
"aa_start": 345,
"aa_end": null,
"aa_length": 443,
"cds_start": 1033,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 1107,
"cdna_end": null,
"cdna_length": 4073,
"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": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "n.*1453C>T",
"hgvs_p": null,
"transcript": "ENST00000543633.5",
"protein_id": "ENSP00000442392.1",
"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": 2019,
"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": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "n.*1471C>T",
"hgvs_p": null,
"transcript": "ENST00000544349.7",
"protein_id": "ENSP00000494419.2",
"transcript_support_level": 2,
"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": 2567,
"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": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "n.*708C>T",
"hgvs_p": null,
"transcript": "ENST00000714044.1",
"protein_id": "ENSP00000519335.1",
"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": 4573,
"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": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "n.*1453C>T",
"hgvs_p": null,
"transcript": "ENST00000543633.5",
"protein_id": "ENSP00000442392.1",
"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": 2019,
"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": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "n.*1471C>T",
"hgvs_p": null,
"transcript": "ENST00000544349.7",
"protein_id": "ENSP00000494419.2",
"transcript_support_level": 2,
"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": 2567,
"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": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"hgvs_c": "n.*708C>T",
"hgvs_p": null,
"transcript": "ENST00000714044.1",
"protein_id": "ENSP00000519335.1",
"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": 4573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VPS33A",
"gene_hgnc_id": 18179,
"dbsnp": "rs767748011",
"frequency_reference_population": 0.000006815374,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000615731,
"gnomad_genomes_af": 0.0000131303,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.885023295879364,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.679,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9957,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.961,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000267199.9",
"gene_symbol": "VPS33A",
"hgnc_id": 18179,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1492C>T",
"hgvs_p": "p.Arg498Trp"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000535844.1",
"gene_symbol": "ENSG00000256861",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1375C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Mucopolysaccharidosis-plus syndrome",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Mucopolysaccharidosis-plus syndrome",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}