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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: 1-107376803-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=107376803&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 107376803,
"ref": "T",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000370068.6",
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NTNG1",
"gene_hgnc_id": 23319,
"hgvs_c": "c.888-18351T>A",
"hgvs_p": null,
"transcript": "NM_001113226.3",
"protein_id": "NP_001106697.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 539,
"cds_start": -4,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6330,
"mane_select": "ENST00000370068.6",
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NTNG1",
"gene_hgnc_id": 23319,
"hgvs_c": "c.888-18351T>A",
"hgvs_p": null,
"transcript": "ENST00000370068.6",
"protein_id": "ENSP00000359085.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 539,
"cds_start": -4,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6330,
"mane_select": "NM_001113226.3",
"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": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NTNG1",
"gene_hgnc_id": 23319,
"hgvs_c": "c.888-18351T>A",
"hgvs_p": null,
"transcript": "ENST00000370066.5",
"protein_id": "ENSP00000359083.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 480,
"cds_start": -4,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1443,
"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": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NTNG1",
"gene_hgnc_id": 23319,
"hgvs_c": "c.888-18351T>A",
"hgvs_p": null,
"transcript": "ENST00000370074.8",
"protein_id": "ENSP00000359091.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 438,
"cds_start": -4,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3048,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NTNG1",
"gene_hgnc_id": 23319,
"hgvs_c": "n.1627-18351T>A",
"hgvs_p": null,
"transcript": "ENST00000294649.8",
"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": 4703,
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NTNG1",
"gene_hgnc_id": 23319,
"hgvs_c": "c.888-18351T>A",
"hgvs_p": null,
"transcript": "NM_001372167.1",
"protein_id": "NP_001359096.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 539,
"cds_start": -4,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6340,
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NTNG1",
"gene_hgnc_id": 23319,
"hgvs_c": "c.888-18351T>A",
"hgvs_p": null,
"transcript": "NM_001372170.1",
"protein_id": "NP_001359099.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 539,
"cds_start": -4,
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"cds_length": 1620,
"cdna_start": null,
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"cdna_length": 6353,
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NTNG1",
"gene_hgnc_id": 23319,
"hgvs_c": "c.888-18351T>A",
"hgvs_p": null,
"transcript": "ENST00000370073.6",
"protein_id": "ENSP00000359090.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 539,
"cds_start": -4,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3347,
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NTNG1",
"gene_hgnc_id": 23319,
"hgvs_c": "c.888-18351T>A",
"hgvs_p": null,
"transcript": "NM_001312688.2",
"protein_id": "NP_001299617.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 505,
"cds_start": -4,
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"cds_length": 1518,
"cdna_start": null,
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"cdna_length": 6238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"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": 6,
"intron_rank": 2,
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"gene_symbol": "NTNG1",
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"hgvs_c": "c.888-18351T>A",
"hgvs_p": null,
"transcript": "ENST00000370065.1",
"protein_id": "ENSP00000359082.1",
"transcript_support_level": 5,
"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": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 7,
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"gene_symbol": "NTNG1",
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"hgvs_c": "c.888-18351T>A",
"hgvs_p": null,
"transcript": "NM_001372166.1",
"protein_id": "NP_001359095.1",
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},
{
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],
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},
{
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],
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"gene_symbol": "NTNG1",
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"hgvs_c": "c.888-18351T>A",
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},
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],
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"gene_symbol": "NTNG1",
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},
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],
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},
{
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],
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"gene_symbol": "NTNG1",
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],
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"gene_symbol": "NTNG1",
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"hgvs_c": "c.888-18351T>A",
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},
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],
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"gene_symbol": "NTNG1",
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"hgvs_c": "c.888-18351T>A",
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"transcript": "NM_014917.4",
"protein_id": "NP_055732.2",
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},
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],
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"gene_symbol": "NTNG1",
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"hgvs_c": "c.888-18351T>A",
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},
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],
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},
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],
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"gene_symbol": "NTNG1",
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"hgvs_c": "c.888-18351T>A",
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"transcript": "XM_017000683.3",
"protein_id": "XP_016856172.1",
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},
{
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],
"exon_rank": null,
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"exon_count": 7,
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"intron_rank_end": null,
"gene_symbol": "NTNG1",
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"hgvs_c": "c.888-18351T>A",
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},
{
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},
{
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"intron_variant"
],
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"gene_symbol": "NTNG1",
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}
],
"gene_symbol": "NTNG1",
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"dbsnp": "rs6677537",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8199999928474426,
"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": -0.82,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.089,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000370068.6",
"gene_symbol": "NTNG1",
"hgnc_id": 23319,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.888-18351T>A",
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}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}