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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: 12-7210243-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=7210243&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 7210243,
"ref": "G",
"alt": "C",
"effect": "3_prime_UTR_variant",
"transcript": "ENST00000675855.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"hgvs_c": "c.*20G>C",
"hgvs_p": null,
"transcript": "NM_001351132.2",
"protein_id": "NP_001338061.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 639,
"cds_start": -4,
"cds_end": null,
"cds_length": 1920,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3237,
"mane_select": "ENST00000675855.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"hgvs_c": "c.*20G>C",
"hgvs_p": null,
"transcript": "ENST00000675855.1",
"protein_id": "ENSP00000502374.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 639,
"cds_start": -4,
"cds_end": null,
"cds_length": 1920,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3237,
"mane_select": "NM_001351132.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"hgvs_c": "c.*20G>C",
"hgvs_p": null,
"transcript": "ENST00000420616.6",
"protein_id": "ENSP00000410159.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 639,
"cds_start": -4,
"cds_end": null,
"cds_length": 1920,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2477,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"hgvs_c": "c.*20G>C",
"hgvs_p": null,
"transcript": "ENST00000266564.7",
"protein_id": "ENSP00000266564.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 631,
"cds_start": -4,
"cds_end": null,
"cds_length": 1896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"hgvs_c": "c.*20G>C",
"hgvs_p": null,
"transcript": "ENST00000266563.9",
"protein_id": "ENSP00000266563.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 602,
"cds_start": -4,
"cds_end": null,
"cds_length": 1809,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"hgvs_c": "c.*20G>C",
"hgvs_p": null,
"transcript": "ENST00000412720.6",
"protein_id": "ENSP00000391601.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 660,
"cds_start": -4,
"cds_end": null,
"cds_length": 1983,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2105,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"hgvs_c": "c.*20G>C",
"hgvs_p": null,
"transcript": "NM_001131023.2",
"protein_id": "NP_001124495.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 654,
"cds_start": -4,
"cds_end": null,
"cds_length": 1965,
"cdna_start": null,
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"cdna_length": 3282,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"hgvs_c": "c.*20G>C",
"hgvs_p": null,
"transcript": "ENST00000434354.6",
"protein_id": "ENSP00000407401.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 654,
"cds_start": -4,
"cds_end": null,
"cds_length": 1965,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2253,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"hgvs_c": "c.*20G>C",
"hgvs_p": null,
"transcript": "NM_001131025.2",
"protein_id": "NP_001124497.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 639,
"cds_start": -4,
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"cds_length": 1920,
"cdna_start": null,
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"cdna_length": 3703,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
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"exon_count": 16,
"intron_rank": null,
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"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"hgvs_c": "c.*20G>C",
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"transcript": "NM_001300789.3",
"protein_id": "NP_001287718.2",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
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"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"hgvs_c": "c.*20G>C",
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"transcript": "NM_001351131.2",
"protein_id": "NP_001338060.1",
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},
{
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"strand": true,
"consequences": [
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],
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"intron_rank": null,
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"gene_symbol": "PEX5",
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},
{
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],
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"gene_symbol": "PEX5",
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"hgvs_c": "c.*20G>C",
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},
{
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],
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"gene_symbol": "PEX5",
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},
{
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],
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},
{
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],
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"gene_symbol": "PEX5",
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],
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},
{
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],
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"transcript": "NM_001351138.2",
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],
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],
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},
{
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"strand": true,
"consequences": [
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],
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"gene_symbol": "PEX5",
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"hgvs_c": "c.*20G>C",
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"transcript": "NM_001351127.2",
"protein_id": "NP_001338056.1",
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},
{
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"consequences": [
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],
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"intron_rank": null,
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"gene_symbol": "PEX5",
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},
{
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"canonical": false,
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"consequences": [
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"intron_variant"
],
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"exon_count": 3,
"intron_rank": 1,
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},
{
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"transcript": "XM_047429257.1",
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},
{
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"splice_donor_variant",
"intron_variant"
],
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"exon_count": 17,
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"gene_symbol": "PEX5",
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},
{
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"splice_donor_variant",
"intron_variant"
],
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"gene_symbol": "PEX5",
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"hgvs_c": "n.2295+1G>C",
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"transcript": "XR_007063107.1",
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"feature": null
}
],
"gene_symbol": "PEX5",
"gene_hgnc_id": 9719,
"dbsnp": "rs145760932",
"frequency_reference_population": 0.00097082916,
"hom_count_reference_population": 9,
"allele_count_reference_population": 1563,
"gnomad_exomes_af": 0.000570774,
"gnomad_genomes_af": 0.00479993,
"gnomad_exomes_ac": 832,
"gnomad_genomes_ac": 731,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 4,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.30000001192092896,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.8600000143051147,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.883,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.7,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.971697303897212,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -15,
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -15,
"benign_score": 16,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000675855.1",
"gene_symbol": "PEX5",
"hgnc_id": 9719,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*20G>C",
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}
],
"clinvar_disease": "Peroxisome biogenesis disorder 2A (Zellweger),not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not specified|Peroxisome biogenesis disorder 2A (Zellweger)",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}