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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: 3-9439909-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=9439909&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 9439909,
"ref": "A",
"alt": "G",
"effect": "intron_variant",
"transcript": "ENST00000402198.7",
"consequences": [
{
"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": 23,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.568-547A>G",
"hgvs_p": null,
"transcript": "NM_001080517.3",
"protein_id": "NP_001073986.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1442,
"cds_start": -4,
"cds_end": null,
"cds_length": 4329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6931,
"mane_select": "ENST00000402198.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.568-547A>G",
"hgvs_p": null,
"transcript": "ENST00000402198.7",
"protein_id": "ENSP00000385852.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1442,
"cds_start": -4,
"cds_end": null,
"cds_length": 4329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6931,
"mane_select": "NM_001080517.3",
"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": 19,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "n.732-547A>G",
"hgvs_p": null,
"transcript": "ENST00000493918.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 4861,
"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": 24,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.625-547A>G",
"hgvs_p": null,
"transcript": "NM_001437635.1",
"protein_id": "NP_001424564.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1480,
"cds_start": -4,
"cds_end": null,
"cds_length": 4443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7037,
"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": 24,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.664-547A>G",
"hgvs_p": null,
"transcript": "NM_001437633.1",
"protein_id": "NP_001424562.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1474,
"cds_start": -4,
"cds_end": null,
"cds_length": 4425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7019,
"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": 24,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.664-547A>G",
"hgvs_p": null,
"transcript": "ENST00000682536.1",
"protein_id": "ENSP00000507956.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1474,
"cds_start": -4,
"cds_end": null,
"cds_length": 4425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5624,
"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": 25,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.568-547A>G",
"hgvs_p": null,
"transcript": "NM_001437643.1",
"protein_id": "NP_001424572.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1461,
"cds_start": -4,
"cds_end": null,
"cds_length": 4386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7515,
"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": 21,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.625-547A>G",
"hgvs_p": null,
"transcript": "ENST00000407969.5",
"protein_id": "ENSP00000384114.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1461,
"cds_start": -4,
"cds_end": null,
"cds_length": 4386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6463,
"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": 24,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.607-547A>G",
"hgvs_p": null,
"transcript": "NM_001437701.1",
"protein_id": "NP_001424630.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1455,
"cds_start": -4,
"cds_end": null,
"cds_length": 4368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 22,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.568-547A>G",
"hgvs_p": null,
"transcript": "ENST00000406341.5",
"protein_id": "ENSP00000383939.1",
"transcript_support_level": 5,
"aa_start": null,
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"aa_length": 1442,
"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": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 25,
"intron_rank": 9,
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"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.274-547A>G",
"hgvs_p": null,
"transcript": "NM_001292043.2",
"protein_id": "NP_001278972.1",
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"cds_start": -4,
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},
{
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"protein_coding": true,
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],
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"exon_count": 26,
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"gene_symbol": "SETD5",
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"hgvs_c": "c.274-547A>G",
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"transcript": "NM_001349451.2",
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},
{
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],
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"gene_symbol": "SETD5",
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"transcript": "ENST00000684055.1",
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},
{
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],
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"gene_symbol": "SETD5",
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"transcript": "ENST00000431285.5",
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},
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],
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"transcript": "ENST00000443339.5",
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},
{
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"strand": true,
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],
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"intron_rank": 6,
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"gene_symbol": "SETD5",
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"transcript": "ENST00000490791.5",
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},
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],
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"transcript": "ENST00000663774.1",
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},
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],
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"intron_rank": 9,
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"gene_symbol": "SETD5",
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"hgvs_c": "n.*634-547A>G",
"hgvs_p": null,
"transcript": "ENST00000665872.1",
"protein_id": "ENSP00000499600.1",
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},
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"strand": true,
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],
"exon_rank": null,
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"exon_count": 28,
"intron_rank": 12,
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"gene_symbol": "SETD5",
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"transcript": "ENST00000666307.1",
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],
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},
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],
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},
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],
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"intron_rank": 9,
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"gene_symbol": "SETD5",
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"hgvs_c": "n.1586-547A>G",
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 19,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "n.1643-547A>G",
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},
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"allele_count_reference_population": 9102,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0599494,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 9102,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 404,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8299999833106995,
"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": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.183,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000402198.7",
"gene_symbol": "SETD5",
"hgnc_id": 25566,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.568-547A>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}