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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: 16-88643560-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=88643560&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 88643560,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_000101.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.381T>C",
"hgvs_p": "p.Arg127Arg",
"transcript": "NM_000101.4",
"protein_id": "NP_000092.2",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 195,
"cds_start": 381,
"cds_end": null,
"cds_length": 588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000261623.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000101.4"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.381T>C",
"hgvs_p": "p.Arg127Arg",
"transcript": "ENST00000261623.8",
"protein_id": "ENSP00000261623.3",
"transcript_support_level": 1,
"aa_start": 127,
"aa_end": null,
"aa_length": 195,
"cds_start": 381,
"cds_end": null,
"cds_length": 588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000101.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261623.8"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.511T>C",
"hgvs_p": "p.Trp171Arg",
"transcript": "ENST00000696161.1",
"protein_id": "ENSP00000512451.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 254,
"cds_start": 511,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696161.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.391T>C",
"hgvs_p": "p.Trp131Arg",
"transcript": "ENST00000565588.6",
"protein_id": "ENSP00000455537.2",
"transcript_support_level": 2,
"aa_start": 131,
"aa_end": null,
"aa_length": 144,
"cds_start": 391,
"cds_end": null,
"cds_length": 437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000565588.6"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.370T>C",
"hgvs_p": "p.Trp124Arg",
"transcript": "ENST00000566229.1",
"protein_id": "ENSP00000457060.1",
"transcript_support_level": 3,
"aa_start": 124,
"aa_end": null,
"aa_length": 129,
"cds_start": 370,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000566229.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.429T>C",
"hgvs_p": "p.Arg143Arg",
"transcript": "ENST00000967613.1",
"protein_id": "ENSP00000637672.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 211,
"cds_start": 429,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967613.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.408T>C",
"hgvs_p": "p.Arg136Arg",
"transcript": "ENST00000696160.1",
"protein_id": "ENSP00000512450.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 204,
"cds_start": 408,
"cds_end": null,
"cds_length": 615,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696160.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.330T>C",
"hgvs_p": "p.Arg110Arg",
"transcript": "ENST00000696163.1",
"protein_id": "ENSP00000512453.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 178,
"cds_start": 330,
"cds_end": null,
"cds_length": 537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696163.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.297T>C",
"hgvs_p": "p.Arg99Arg",
"transcript": "ENST00000696156.1",
"protein_id": "ENSP00000512446.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 167,
"cds_start": 297,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696156.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.234T>C",
"hgvs_p": "p.Arg78Arg",
"transcript": "ENST00000967612.1",
"protein_id": "ENSP00000637671.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 146,
"cds_start": 234,
"cds_end": null,
"cds_length": 441,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967612.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.*1100T>C",
"hgvs_p": null,
"transcript": "ENST00000696162.1",
"protein_id": "ENSP00000512452.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 176,
"cds_start": null,
"cds_end": null,
"cds_length": 531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696162.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.*304T>C",
"hgvs_p": null,
"transcript": "ENST00000696159.1",
"protein_id": "ENSP00000512449.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 175,
"cds_start": null,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696159.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.*635T>C",
"hgvs_p": null,
"transcript": "ENST00000696158.1",
"protein_id": "ENSP00000512448.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 153,
"cds_start": null,
"cds_end": null,
"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696158.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.*598T>C",
"hgvs_p": null,
"transcript": "ENST00000696157.1",
"protein_id": "ENSP00000512447.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 129,
"cds_start": null,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696157.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "c.*1606T>C",
"hgvs_p": null,
"transcript": "XM_011522905.4",
"protein_id": "XP_011521207.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 210,
"cds_start": null,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011522905.4"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"hgvs_c": "n.960T>C",
"hgvs_p": null,
"transcript": "ENST00000566534.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000566534.5"
}
],
"gene_symbol": "CYBA",
"gene_hgnc_id": 2577,
"dbsnp": "rs12123",
"frequency_reference_population": 0.03250272,
"hom_count_reference_population": 1029,
"allele_count_reference_population": 49824,
"gnomad_exomes_af": 0.0333483,
"gnomad_genomes_af": 0.0248174,
"gnomad_exomes_ac": 46053,
"gnomad_genomes_ac": 3771,
"gnomad_exomes_homalt": 955,
"gnomad_genomes_homalt": 74,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006692230701446533,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.5731,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.96,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.717,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000101.4",
"gene_symbol": "CYBA",
"hgnc_id": 2577,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.381T>C",
"hgvs_p": "p.Arg127Arg"
}
],
"clinvar_disease": " autosomal recessive, chronic, cytochrome b-negative,Chronic granulomatous disease,Granulomatous disease,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|Granulomatous disease, chronic, autosomal recessive, cytochrome b-negative|Chronic granulomatous disease|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}