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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: 3-181712418-GGCGGCGGCGGCAACTCCACC-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=181712418&ref=GGCGGCGGCGGCAACTCCACC&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 181712418,
"ref": "GGCGGCGGCGGCAACTCCACC",
"alt": "G",
"effect": "frameshift_variant",
"transcript": "ENST00000325404.3",
"consequences": [
{
"aa_ref": "NSTAAAA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOX2",
"gene_hgnc_id": 11195,
"hgvs_c": "c.70_89delAACTCCACCGCGGCGGCGGC",
"hgvs_p": "p.Asn24fs",
"transcript": "NM_003106.4",
"protein_id": "NP_003097.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 317,
"cds_start": 70,
"cds_end": null,
"cds_length": 954,
"cdna_start": 506,
"cdna_end": null,
"cdna_length": 2512,
"mane_select": "ENST00000325404.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NSTAAAA",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOX2",
"gene_hgnc_id": 11195,
"hgvs_c": "c.70_89delAACTCCACCGCGGCGGCGGC",
"hgvs_p": "p.Asn24fs",
"transcript": "ENST00000325404.3",
"protein_id": "ENSP00000323588.1",
"transcript_support_level": 6,
"aa_start": 24,
"aa_end": null,
"aa_length": 317,
"cds_start": 70,
"cds_end": null,
"cds_length": 954,
"cdna_start": 506,
"cdna_end": null,
"cdna_length": 2512,
"mane_select": "NM_003106.4",
"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": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.349+12547_349+12566delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000466034.7",
"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": 1772,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.482-27139_482-27120delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000476964.6",
"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": 3226,
"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": 4,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.593+12547_593+12566delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000491282.6",
"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": 1040,
"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": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.541-2755_541-2736delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000498731.6",
"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": 3964,
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.708+12547_708+12566delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000460739.6",
"protein_id": null,
"transcript_support_level": 4,
"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": 1479,
"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": 4,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.473-27139_473-27120delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000469278.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 561,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.391+12547_391+12566delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000477928.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 902,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.309-27139_309-27120delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000485035.4",
"protein_id": null,
"transcript_support_level": 4,
"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": 1581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.355-2755_355-2736delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000492337.6",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2184,
"mane_select": null,
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"feature": null
},
{
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"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.782+12547_782+12566delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000493521.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1239,
"mane_select": null,
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 3,
"intron_rank": 2,
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"gene_symbol": "SOX2-OT",
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"hgvs_c": "n.289-78243_289-78224delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000498226.6",
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"cds_start": -4,
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"mane_select": null,
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},
{
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],
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"gene_symbol": "SOX2-OT",
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},
{
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"strand": true,
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],
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"exon_count": 4,
"intron_rank": 1,
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"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.287-2755_287-2736delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
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},
{
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],
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"gene_symbol": "SOX2-OT",
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},
{
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],
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"gene_symbol": "SOX2-OT",
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"hgvs_c": "n.286+12547_286+12566delAACTCCACCGCGGCGGCGGC",
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},
{
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],
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"intron_rank": 1,
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"gene_symbol": "SOX2-OT",
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"hgvs_c": "n.661+12547_661+12566delAACTCCACCGCGGCGGCGGC",
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},
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],
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"gene_symbol": "SOX2-OT",
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},
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],
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},
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],
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},
{
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"strand": true,
"consequences": [
"intron_variant"
],
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"exon_count": 2,
"intron_rank": 1,
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"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.47+12786_47+12805delAACTCCACCGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000599082.2",
"protein_id": null,
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},
{
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],
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"exon_count": 4,
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{
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{
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],
"clinvar_disease": "Anophthalmia/microphthalmia-esophageal atresia syndrome,SOX2-related disorder,Septo-optic dysplasia sequence,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:10",
"phenotype_combined": "not provided|Anophthalmia/microphthalmia-esophageal atresia syndrome|SOX2-related disorder|Septo-optic dysplasia sequence",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}