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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: X-37805098-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=37805098&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 37805098,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000378588.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBB",
"gene_hgnc_id": 2578,
"hgvs_c": "c.1244C>G",
"hgvs_p": "p.Pro415Arg",
"transcript": "NM_000397.4",
"protein_id": "NP_000388.2",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 570,
"cds_start": 1244,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 1263,
"cdna_end": null,
"cdna_length": 4276,
"mane_select": "ENST00000378588.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBB",
"gene_hgnc_id": 2578,
"hgvs_c": "c.1244C>G",
"hgvs_p": "p.Pro415Arg",
"transcript": "ENST00000378588.5",
"protein_id": "ENSP00000367851.4",
"transcript_support_level": 1,
"aa_start": 415,
"aa_end": null,
"aa_length": 570,
"cds_start": 1244,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 1263,
"cdna_end": null,
"cdna_length": 4276,
"mane_select": "NM_000397.4",
"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": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250349",
"gene_hgnc_id": null,
"hgvs_c": "c.171+379098C>G",
"hgvs_p": null,
"transcript": "ENST00000465127.1",
"protein_id": "ENSP00000417050.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 279,
"cds_start": -4,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBB",
"gene_hgnc_id": 2578,
"hgvs_c": "c.1148C>G",
"hgvs_p": "p.Pro383Arg",
"transcript": "ENST00000696171.1",
"protein_id": "ENSP00000512462.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 538,
"cds_start": 1148,
"cds_end": null,
"cds_length": 1617,
"cdna_start": 1167,
"cdna_end": null,
"cdna_length": 1822,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBB",
"gene_hgnc_id": 2578,
"hgvs_c": "c.938C>G",
"hgvs_p": "p.Pro313Arg",
"transcript": "XM_047441855.1",
"protein_id": "XP_047297811.1",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 468,
"cds_start": 938,
"cds_end": null,
"cds_length": 1407,
"cdna_start": 1236,
"cdna_end": null,
"cdna_length": 4249,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBB",
"gene_hgnc_id": 2578,
"hgvs_c": "n.*753C>G",
"hgvs_p": null,
"transcript": "ENST00000696170.1",
"protein_id": "ENSP00000512461.1",
"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": 4171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBB",
"gene_hgnc_id": 2578,
"hgvs_c": "n.*753C>G",
"hgvs_p": null,
"transcript": "ENST00000696170.1",
"protein_id": "ENSP00000512461.1",
"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": 4171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CYBB",
"gene_hgnc_id": 2578,
"dbsnp": "rs137854585",
"frequency_reference_population": 0.000008925065,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000892507,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9955300092697144,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.976,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9988,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.81,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.565,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000378588.5",
"gene_symbol": "CYBB",
"hgnc_id": 2578,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AR,Unknown",
"hgvs_c": "c.1244C>G",
"hgvs_p": "p.Pro415Arg"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000465127.1",
"gene_symbol": "ENSG00000250349",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.171+379098C>G",
"hgvs_p": null
}
],
"clinvar_disease": " X-linked, chronic,Granulomatous disease",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Granulomatous disease, chronic, X-linked",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}