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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: 5-112707883-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=112707883&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 112707883,
"ref": "G",
"alt": "A",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_001407446.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.165+1G>A",
"hgvs_p": null,
"transcript": "NM_001407446.1",
"protein_id": "NP_001394375.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2871,
"cds_start": -4,
"cds_end": null,
"cds_length": 8616,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.-19+1G>A",
"hgvs_p": null,
"transcript": "NM_001407447.1",
"protein_id": "NP_001394376.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2861,
"cds_start": -4,
"cds_end": null,
"cds_length": 8586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11102,
"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": 17,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.-19+234G>A",
"hgvs_p": null,
"transcript": "NM_001407448.1",
"protein_id": "NP_001394377.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2861,
"cds_start": -4,
"cds_end": null,
"cds_length": 8586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.165+1G>A",
"hgvs_p": null,
"transcript": "NM_001354897.2",
"protein_id": "NP_001341826.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2853,
"cds_start": -4,
"cds_end": null,
"cds_length": 8562,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.-19+1G>A",
"hgvs_p": null,
"transcript": "NM_001354895.2",
"protein_id": "NP_001341824.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2843,
"cds_start": -4,
"cds_end": null,
"cds_length": 8532,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11048,
"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": 16,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.-19+234G>A",
"hgvs_p": null,
"transcript": "NM_001407450.1",
"protein_id": "NP_001394379.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2843,
"cds_start": -4,
"cds_end": null,
"cds_length": 8532,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10815,
"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": 16,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.-19+234G>A",
"hgvs_p": null,
"transcript": "ENST00000509732.6",
"protein_id": "ENSP00000426541.2",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 2843,
"cds_start": -4,
"cds_end": null,
"cds_length": 8532,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.-19+1G>A",
"hgvs_p": null,
"transcript": "NM_001407452.1",
"protein_id": "NP_001394381.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2833,
"cds_start": -4,
"cds_end": null,
"cds_length": 8502,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11018,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.165+1G>A",
"hgvs_p": null,
"transcript": "NM_001127511.3",
"protein_id": "NP_001120983.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2825,
"cds_start": -4,
"cds_end": null,
"cds_length": 8478,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.165+1G>A",
"hgvs_p": null,
"transcript": "ENST00000507379.6",
"protein_id": "ENSP00000423224.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 2825,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.-43+234G>A",
"hgvs_p": null,
"transcript": "NM_001407453.1",
"protein_id": "NP_001394382.1",
"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": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
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"exon_count": 17,
"intron_rank": 1,
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"gene_symbol": "APC",
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"hgvs_c": "c.-19+1G>A",
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"transcript": "NM_001407456.1",
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},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
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"exon_count": 17,
"intron_rank": 1,
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"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.-19+234G>A",
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"transcript": "NM_001407457.1",
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},
{
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"protein_coding": true,
"strand": true,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"intron_rank": 1,
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"gene_symbol": "APC",
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"hgvs_c": "c.165+1G>A",
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"transcript": "NM_001354902.2",
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},
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],
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"intron_rank": 1,
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"gene_symbol": "APC",
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"hgvs_c": "c.-19+234G>A",
"hgvs_p": null,
"transcript": "NM_001407458.1",
"protein_id": "NP_001394387.1",
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},
{
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"strand": true,
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"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
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"intron_rank": 1,
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"gene_symbol": "APC",
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"hgvs_c": "c.-19+1G>A",
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},
{
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"intron_variant"
],
"exon_rank": null,
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"gene_symbol": "APC",
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"hgvs_c": "c.-19+1G>A",
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"transcript": "NM_001407469.1",
"protein_id": "NP_001394398.1",
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},
{
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"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
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"exon_count": 17,
"intron_rank": 1,
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"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.-1054+1G>A",
"hgvs_p": null,
"transcript": "NM_001407470.1",
"protein_id": "NP_001394399.1",
"transcript_support_level": null,
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},
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"intron_variant"
],
"exon_rank": null,
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"intron_rank": 1,
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"hgvs_c": "c.-1054+1G>A",
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},
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"strand": true,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"intron_rank": 1,
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"gene_symbol": "APC",
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"hgvs_c": "n.165+1G>A",
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"transcript": "ENST00000505350.2",
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},
{
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"strand": true,
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"intron_variant"
],
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"intron_rank": 1,
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"gene_symbol": "APC",
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"transcript": "ENST00000713636.1",
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "n.152+234G>A",
"hgvs_p": null,
"transcript": "NR_176365.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "n.385+1G>A",
"hgvs_p": null,
"transcript": "NR_176366.1",
"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": 10899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"dbsnp": "rs1239946140",
"frequency_reference_population": 0.000008770212,
"hom_count_reference_population": 0,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.00000657784,
"gnomad_genomes_af": 0.0000263047,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.27000001072883606,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.8859999775886536,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.262,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": 0.988451337246128,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PVS1"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001407446.1",
"gene_symbol": "APC",
"hgnc_id": 583,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.165+1G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Familial adenomatous polyposis 1,Hereditary cancer-predisposing syndrome,Neoplasm",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Hereditary cancer-predisposing syndrome|Familial adenomatous polyposis 1|Neoplasm",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}