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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-134500030-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=134500030&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 134500030,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_000194.3",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.His204Tyr",
"transcript": "NM_000194.3",
"protein_id": "NP_000185.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 218,
"cds_start": 610,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000298556.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000194.3"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.His204Tyr",
"transcript": "ENST00000298556.8",
"protein_id": "ENSP00000298556.7",
"transcript_support_level": 1,
"aa_start": 204,
"aa_end": null,
"aa_length": 218,
"cds_start": 610,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000194.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000298556.8"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.655C>T",
"hgvs_p": "p.His219Tyr",
"transcript": "ENST00000969780.1",
"protein_id": "ENSP00000639839.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 233,
"cds_start": 655,
"cds_end": null,
"cds_length": 702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969780.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.646C>T",
"hgvs_p": "p.His216Tyr",
"transcript": "ENST00000969779.1",
"protein_id": "ENSP00000639838.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 230,
"cds_start": 646,
"cds_end": null,
"cds_length": 693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969779.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.601C>T",
"hgvs_p": "p.His201Tyr",
"transcript": "ENST00000916520.1",
"protein_id": "ENSP00000586579.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 215,
"cds_start": 601,
"cds_end": null,
"cds_length": 648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916520.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.592C>T",
"hgvs_p": "p.His198Tyr",
"transcript": "ENST00000916519.1",
"protein_id": "ENSP00000586578.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 212,
"cds_start": 592,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916519.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.544C>T",
"hgvs_p": "p.His182Tyr",
"transcript": "ENST00000969781.1",
"protein_id": "ENSP00000639840.1",
"transcript_support_level": null,
"aa_start": 182,
"aa_end": null,
"aa_length": 196,
"cds_start": 544,
"cds_end": null,
"cds_length": 591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969781.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.319C>T",
"hgvs_p": "p.His107Tyr",
"transcript": "ENST00000883913.1",
"protein_id": "ENSP00000553972.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 121,
"cds_start": 319,
"cds_end": null,
"cds_length": 366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883913.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.319C>T",
"hgvs_p": "p.His107Tyr",
"transcript": "ENST00000883914.1",
"protein_id": "ENSP00000553973.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 121,
"cds_start": 319,
"cds_end": null,
"cds_length": 366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883914.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "n.567+1346C>T",
"hgvs_p": null,
"transcript": "ENST00000475720.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "pseudogene",
"feature": "ENST00000475720.1"
}
],
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"dbsnp": "rs137852490",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9894636273384094,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.6600000262260437,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.85,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9476,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.69,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.216,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.08,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.83196013608141,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 13,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 13,
"benign_score": 0,
"pathogenic_score": 13,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_000194.3",
"gene_symbol": "HPRT1",
"hgnc_id": 5157,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.610C>T",
"hgvs_p": "p.His204Tyr"
}
],
"clinvar_disease": "Lesch-Nyhan syndrome,Partial hypoxanthine-guanine phosphoribosyltransferase deficiency",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Partial hypoxanthine-guanine phosphoribosyltransferase deficiency;Lesch-Nyhan syndrome",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}