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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-107642407-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=107642407&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 107642407,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000372435.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.447G>A",
"hgvs_p": "p.Pro149Pro",
"transcript": "NM_002764.4",
"protein_id": "NP_002755.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 318,
"cds_start": 447,
"cds_end": null,
"cds_length": 957,
"cdna_start": 566,
"cdna_end": null,
"cdna_length": 2070,
"mane_select": "ENST00000372435.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.447G>A",
"hgvs_p": "p.Pro149Pro",
"transcript": "ENST00000372435.10",
"protein_id": "ENSP00000361512.4",
"transcript_support_level": 1,
"aa_start": 149,
"aa_end": null,
"aa_length": 318,
"cds_start": 447,
"cds_end": null,
"cds_length": 957,
"cdna_start": 566,
"cdna_end": null,
"cdna_length": 2070,
"mane_select": "NM_002764.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.447G>A",
"hgvs_p": "p.Pro149Pro",
"transcript": "ENST00000643795.2",
"protein_id": "ENSP00000496286.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 321,
"cds_start": 447,
"cds_end": null,
"cds_length": 966,
"cdna_start": 648,
"cdna_end": null,
"cdna_length": 1450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.348G>A",
"hgvs_p": "p.Pro116Pro",
"transcript": "ENST00000372418.4",
"protein_id": "ENSP00000361495.2",
"transcript_support_level": 3,
"aa_start": 116,
"aa_end": null,
"aa_length": 285,
"cds_start": 348,
"cds_end": null,
"cds_length": 858,
"cdna_start": 487,
"cdna_end": null,
"cdna_length": 1434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.42G>A",
"hgvs_p": "p.Pro14Pro",
"transcript": "ENST00000675082.1",
"protein_id": "ENSP00000502347.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 94,
"cds_start": 42,
"cds_end": null,
"cds_length": 285,
"cdna_start": 42,
"cdna_end": null,
"cdna_length": 285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.42G>A",
"hgvs_p": "p.Pro14Pro",
"transcript": "ENST00000675921.1",
"protein_id": "ENSP00000502707.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 91,
"cds_start": 42,
"cds_end": null,
"cds_length": 278,
"cdna_start": 42,
"cdna_end": null,
"cdna_length": 278,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.541G>A",
"hgvs_p": null,
"transcript": "ENST00000645903.1",
"protein_id": null,
"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": 672,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*140G>A",
"hgvs_p": null,
"transcript": "ENST00000674826.1",
"protein_id": "ENSP00000502278.1",
"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": 996,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.42G>A",
"hgvs_p": null,
"transcript": "ENST00000675124.1",
"protein_id": "ENSP00000502439.1",
"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": 527,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.42G>A",
"hgvs_p": null,
"transcript": "ENST00000675630.1",
"protein_id": "ENSP00000502050.1",
"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": 523,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*31G>A",
"hgvs_p": null,
"transcript": "ENST00000675720.1",
"protein_id": "ENSP00000501721.1",
"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": 580,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*140G>A",
"hgvs_p": null,
"transcript": "ENST00000674826.1",
"protein_id": "ENSP00000502278.1",
"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": 996,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*31G>A",
"hgvs_p": null,
"transcript": "ENST00000675720.1",
"protein_id": "ENSP00000501721.1",
"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": 580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.358+1454G>A",
"hgvs_p": null,
"transcript": "ENST00000676092.1",
"protein_id": "ENSP00000502780.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 121,
"cds_start": -4,
"cds_end": null,
"cds_length": 366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 487,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.-82-2770G>A",
"hgvs_p": null,
"transcript": "NM_001204402.2",
"protein_id": "NP_001191331.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 114,
"cds_start": -4,
"cds_end": null,
"cds_length": 345,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1662,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.123-2770G>A",
"hgvs_p": null,
"transcript": "ENST00000644642.1",
"protein_id": "ENSP00000495493.1",
"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": 1515,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.490+1407G>A",
"hgvs_p": null,
"transcript": "ENST00000674525.1",
"protein_id": null,
"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": 883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.184-2770G>A",
"hgvs_p": null,
"transcript": "ENST00000675046.1",
"protein_id": "ENSP00000501767.1",
"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": 518,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"dbsnp": "rs80338730",
"frequency_reference_population": 0.00048017877,
"hom_count_reference_population": 193,
"allele_count_reference_population": 581,
"gnomad_exomes_af": 0.000435375,
"gnomad_genomes_af": 0.000919126,
"gnomad_exomes_ac": 478,
"gnomad_genomes_ac": 103,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.36000001430511475,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.653,
"phylop100way_prediction": "Benign",
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000372435.10",
"gene_symbol": "PRPS1",
"hgnc_id": 9462,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.447G>A",
"hgvs_p": "p.Pro149Pro"
}
],
"clinvar_disease": " X-linked 1,Arts syndrome,Charcot-Marie-Tooth Neuropathy X,Charcot-Marie-Tooth disease X-linked recessive 5,Hearing loss,History of neurodevelopmental disorder,Phosphoribosylpyrophosphate synthetase superactivity,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:5 O:1",
"phenotype_combined": "Arts syndrome|not provided|Phosphoribosylpyrophosphate synthetase superactivity|Hearing loss, X-linked 1|not specified|Charcot-Marie-Tooth Neuropathy X|History of neurodevelopmental disorder|Hearing loss, X-linked 1;Charcot-Marie-Tooth disease X-linked recessive 5;Phosphoribosylpyrophosphate synthetase superactivity;Arts syndrome",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}