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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-134486471-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=134486471&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PP3",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "HPRT1",
"hgnc_id": 5157,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Gln109*",
"inheritance_mode": "XL",
"pathogenic_score": 17,
"score": 17,
"transcript": "NM_000194.3",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP3,PP5_Very_Strong",
"acmg_score": 17,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.63,
"chr": "X",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Lesch-Nyhan syndrome,Partial hypoxanthine-guanine phosphoribosyltransferase deficiency,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6299999952316284,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 218,
"aa_ref": "Q",
"aa_start": 109,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1395,
"cdna_start": 472,
"cds_end": null,
"cds_length": 657,
"cds_start": 325,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_000194.3",
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Gln109*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000298556.8",
"protein_coding": true,
"protein_id": "NP_000185.1",
"strand": true,
"transcript": "NM_000194.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 218,
"aa_ref": "Q",
"aa_start": 109,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1395,
"cdna_start": 472,
"cds_end": null,
"cds_length": 657,
"cds_start": 325,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000298556.8",
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Gln109*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000194.3",
"protein_coding": true,
"protein_id": "ENSP00000298556.7",
"strand": true,
"transcript": "ENST00000298556.8",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 233,
"aa_ref": "Q",
"aa_start": 124,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1401,
"cdna_start": 488,
"cds_end": null,
"cds_length": 702,
"cds_start": 370,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000969780.1",
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"hgvs_c": "c.370C>T",
"hgvs_p": "p.Gln124*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639839.1",
"strand": true,
"transcript": "ENST00000969780.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 230,
"aa_ref": "Q",
"aa_start": 109,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1439,
"cdna_start": 482,
"cds_end": null,
"cds_length": 693,
"cds_start": 325,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000969779.1",
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Gln109*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639838.1",
"strand": true,
"transcript": "ENST00000969779.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 212,
"aa_ref": "Q",
"aa_start": 109,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1393,
"cdna_start": 480,
"cds_end": null,
"cds_length": 639,
"cds_start": 325,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000916519.1",
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Gln109*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586578.1",
"strand": true,
"transcript": "ENST00000916519.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 121,
"aa_ref": "Q",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1077,
"cdna_start": 154,
"cds_end": null,
"cds_length": 366,
"cds_start": 34,
"consequences": [
"stop_gained"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000883913.1",
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"hgvs_c": "c.34C>T",
"hgvs_p": "p.Gln12*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000553972.1",
"strand": true,
"transcript": "ENST00000883913.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 215,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1275,
"cdna_start": null,
"cds_end": null,
"cds_length": 648,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000916520.1",
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"hgvs_c": "c.319-3C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586579.1",
"strand": true,
"transcript": "ENST00000916520.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 196,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1210,
"cdna_start": null,
"cds_end": null,
"cds_length": 591,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000969781.1",
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"hgvs_c": "c.319-3717C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639840.1",
"strand": true,
"transcript": "ENST00000969781.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 121,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1063,
"cdna_start": null,
"cds_end": null,
"cds_length": 366,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000883914.1",
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"hgvs_c": "c.318+11107C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000553973.1",
"strand": true,
"transcript": "ENST00000883914.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 724,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000462974.5",
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"hgvs_c": "n.483C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000462974.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 599,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000475720.1",
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"hgvs_c": "n.283C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000475720.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs137852489",
"effect": "stop_gained",
"frequency_reference_population": null,
"gene_hgnc_id": 5157,
"gene_symbol": "HPRT1",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Lesch-Nyhan syndrome|Lesch-Nyhan syndrome;Partial hypoxanthine-guanine phosphoribosyltransferase deficiency|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.301,
"pos": 134486471,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.5099999904632568,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.51,
"transcript": "NM_000194.3"
}
]
}