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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: 16-88648099-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=88648099&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 88648099,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000261623.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "NM_000101.4",
"protein_id": "NP_000092.2",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 195,
"cds_start": 74,
"cds_end": null,
"cds_length": 588,
"cdna_start": 114,
"cdna_end": null,
"cdna_length": 692,
"mane_select": "ENST00000261623.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000261623.8",
"protein_id": "ENSP00000261623.3",
"transcript_support_level": 1,
"aa_start": 25,
"aa_end": null,
"aa_length": 195,
"cds_start": 74,
"cds_end": null,
"cds_length": 588,
"cdna_start": 114,
"cdna_end": null,
"cdna_length": 692,
"mane_select": "NM_000101.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000569359.5",
"protein_id": "ENSP00000456079.1",
"transcript_support_level": 1,
"aa_start": 25,
"aa_end": null,
"aa_length": 128,
"cds_start": 74,
"cds_end": null,
"cds_length": 387,
"cdna_start": 91,
"cdna_end": null,
"cdna_length": 1415,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000696161.1",
"protein_id": "ENSP00000512451.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 254,
"cds_start": 74,
"cds_end": null,
"cds_length": 765,
"cdna_start": 139,
"cdna_end": null,
"cdna_length": 846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000567174.5",
"protein_id": "ENSP00000454951.1",
"transcript_support_level": 2,
"aa_start": 25,
"aa_end": null,
"aa_length": 210,
"cds_start": 74,
"cds_end": null,
"cds_length": 633,
"cdna_start": 102,
"cdna_end": null,
"cdna_length": 1085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000696160.1",
"protein_id": "ENSP00000512450.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 204,
"cds_start": 74,
"cds_end": null,
"cds_length": 615,
"cdna_start": 142,
"cdna_end": null,
"cdna_length": 747,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000696163.1",
"protein_id": "ENSP00000512453.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 178,
"cds_start": 74,
"cds_end": null,
"cds_length": 537,
"cdna_start": 144,
"cdna_end": null,
"cdna_length": 670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000696162.1",
"protein_id": "ENSP00000512452.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 176,
"cds_start": 74,
"cds_end": null,
"cds_length": 531,
"cdna_start": 142,
"cdna_end": null,
"cdna_length": 1969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000696159.1",
"protein_id": "ENSP00000512449.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 175,
"cds_start": 74,
"cds_end": null,
"cds_length": 528,
"cdna_start": 142,
"cdna_end": null,
"cdna_length": 1171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000696156.1",
"protein_id": "ENSP00000512446.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 167,
"cds_start": 74,
"cds_end": null,
"cds_length": 504,
"cdna_start": 142,
"cdna_end": null,
"cdna_length": 650,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000696158.1",
"protein_id": "ENSP00000512448.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 153,
"cds_start": 74,
"cds_end": null,
"cds_length": 462,
"cdna_start": 135,
"cdna_end": null,
"cdna_length": 1429,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000565588.6",
"protein_id": "ENSP00000455537.2",
"transcript_support_level": 2,
"aa_start": 25,
"aa_end": null,
"aa_length": 144,
"cds_start": 74,
"cds_end": null,
"cds_length": 437,
"cdna_start": 139,
"cdna_end": null,
"cdna_length": 502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000568278.1",
"protein_id": "ENSP00000455506.1",
"transcript_support_level": 5,
"aa_start": 25,
"aa_end": null,
"aa_length": 144,
"cds_start": 74,
"cds_end": null,
"cds_length": 437,
"cdna_start": 76,
"cdna_end": null,
"cdna_length": 439,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "ENST00000696157.1",
"protein_id": "ENSP00000512447.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 129,
"cds_start": 74,
"cds_end": null,
"cds_length": 390,
"cdna_start": 135,
"cdna_end": null,
"cdna_length": 1320,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp",
"transcript": "XM_011522905.4",
"protein_id": "XP_011521207.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 210,
"cds_start": 74,
"cds_end": null,
"cds_length": 633,
"cdna_start": 114,
"cdna_end": null,
"cdna_length": 2550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Gly21Gly",
"transcript": "ENST00000566229.1",
"protein_id": "ENSP00000457060.1",
"transcript_support_level": 3,
"aa_start": 21,
"aa_end": null,
"aa_length": 129,
"cds_start": 63,
"cds_end": null,
"cds_length": 390,
"cdna_start": 78,
"cdna_end": null,
"cdna_length": 405,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "n.92G>A",
"hgvs_p": null,
"transcript": "ENST00000562209.1",
"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": 624,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "n.49G>A",
"hgvs_p": null,
"transcript": "ENST00000563526.5",
"protein_id": null,
"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": 1052,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "n.96G>A",
"hgvs_p": null,
"transcript": "ENST00000566534.5",
"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": 1006,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"dbsnp": "rs179363891",
"frequency_reference_population": 0.0000024811834,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000205491,
"gnomad_genomes_af": 0.00000656953,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9887895584106445,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.907,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9964,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.41,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.701,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.1,
"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_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000261623.8",
"gene_symbol": "CYBA",
"hgnc_id": 2577,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Gly25Asp"
}
],
"clinvar_disease": " autosomal recessive, chronic, cytochrome b-negative,Granulomatous disease,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "not specified|Granulomatous disease, chronic, autosomal recessive, cytochrome b-negative|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}