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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: 22-18925164-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=18925164&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 18925164,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000357068.11",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.554G>A",
"hgvs_p": "p.Trp185*",
"transcript": "NM_016335.6",
"protein_id": "NP_057419.5",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 600,
"cds_start": 554,
"cds_end": null,
"cds_length": 1803,
"cdna_start": 560,
"cdna_end": null,
"cdna_length": 2203,
"mane_select": "ENST00000357068.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.554G>A",
"hgvs_p": "p.Trp185*",
"transcript": "ENST00000357068.11",
"protein_id": "ENSP00000349577.6",
"transcript_support_level": 1,
"aa_start": 185,
"aa_end": null,
"aa_length": 600,
"cds_start": 554,
"cds_end": null,
"cds_length": 1803,
"cdna_start": 560,
"cdna_end": null,
"cdna_length": 2203,
"mane_select": "NM_016335.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.554G>A",
"hgvs_p": "p.Trp185*",
"transcript": "ENST00000610940.4",
"protein_id": "ENSP00000480347.1",
"transcript_support_level": 1,
"aa_start": 185,
"aa_end": null,
"aa_length": 600,
"cds_start": 554,
"cds_end": null,
"cds_length": 1803,
"cdna_start": 758,
"cdna_end": null,
"cdna_length": 2405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.230G>A",
"hgvs_p": "p.Trp77*",
"transcript": "ENST00000334029.6",
"protein_id": "ENSP00000334726.2",
"transcript_support_level": 1,
"aa_start": 77,
"aa_end": null,
"aa_length": 492,
"cds_start": 230,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 343,
"cdna_end": null,
"cdna_length": 1985,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "n.409G>A",
"hgvs_p": null,
"transcript": "ENST00000482858.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 4676,
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "n.562G>A",
"hgvs_p": null,
"transcript": "ENST00000491604.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 3106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000283809",
"gene_hgnc_id": null,
"hgvs_c": "c.513+14136C>T",
"hgvs_p": null,
"transcript": "ENST00000638240.1",
"protein_id": "ENSP00000492446.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 180,
"cds_start": -4,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.230G>A",
"hgvs_p": "p.Trp77*",
"transcript": "NM_001195226.2",
"protein_id": "NP_001182155.2",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 492,
"cds_start": 230,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 445,
"cdna_end": null,
"cdna_length": 2088,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.230G>A",
"hgvs_p": "p.Trp77*",
"transcript": "NM_001368250.2",
"protein_id": "NP_001355179.2",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 492,
"cds_start": 230,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 405,
"cdna_end": null,
"cdna_length": 2048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.230G>A",
"hgvs_p": "p.Trp77*",
"transcript": "ENST00000420436.5",
"protein_id": "ENSP00000410805.1",
"transcript_support_level": 2,
"aa_start": 77,
"aa_end": null,
"aa_length": 492,
"cds_start": 230,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 391,
"cdna_end": null,
"cdna_length": 2034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.77G>A",
"hgvs_p": "p.Trp26*",
"transcript": "ENST00000450579.1",
"protein_id": "ENSP00000396806.1",
"transcript_support_level": 3,
"aa_start": 26,
"aa_end": null,
"aa_length": 134,
"cds_start": 77,
"cds_end": null,
"cds_length": 405,
"cdna_start": 266,
"cdna_end": null,
"cdna_length": 594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Arg",
"transcript": "ENST00000438924.5",
"protein_id": "ENSP00000409742.1",
"transcript_support_level": 3,
"aa_start": 67,
"aa_end": null,
"aa_length": 183,
"cds_start": 199,
"cds_end": null,
"cds_length": 552,
"cdna_start": 200,
"cdna_end": null,
"cdna_length": 553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "c.322G>A",
"hgvs_p": "p.Gly108Arg",
"transcript": "ENST00000457083.1",
"protein_id": "ENSP00000413941.1",
"transcript_support_level": 3,
"aa_start": 108,
"aa_end": null,
"aa_length": 162,
"cds_start": 322,
"cds_end": null,
"cds_length": 489,
"cdna_start": 324,
"cdna_end": null,
"cdna_length": 491,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"hgvs_c": "n.193G>A",
"hgvs_p": null,
"transcript": "ENST00000496625.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRODH",
"gene_hgnc_id": 9453,
"dbsnp": "rs11913840",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0.0000378472,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.029999999329447746,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": -0.056,
"phylop100way_prediction": "Benign",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1,BP6_Very_Strong",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 8,
"pathogenic_score": 8,
"criteria": [
"PVS1",
"BP6_Very_Strong"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000357068.11",
"gene_symbol": "PRODH",
"hgnc_id": 9453,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.554G>A",
"hgvs_p": "p.Trp185*"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000638240.1",
"gene_symbol": "ENSG00000283809",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.513+14136C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Proline dehydrogenase deficiency,Schizophrenia 4,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "Schizophrenia 4;Proline dehydrogenase deficiency|not provided|Proline dehydrogenase deficiency",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}