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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: 12-23543182-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=23543182&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 23543182,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000451604.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "SOX5",
"gene_hgnc_id": 11201,
"hgvs_c": "c.1771+29G>A",
"hgvs_p": null,
"transcript": "NM_006940.6",
"protein_id": "NP_008871.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 763,
"cds_start": -4,
"cds_end": null,
"cds_length": 2292,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7076,
"mane_select": "ENST00000451604.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "SOX5",
"gene_hgnc_id": 11201,
"hgvs_c": "c.1771+29G>A",
"hgvs_p": null,
"transcript": "ENST00000451604.7",
"protein_id": "ENSP00000398273.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 763,
"cds_start": -4,
"cds_end": null,
"cds_length": 2292,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7076,
"mane_select": "NM_006940.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SOX5",
"gene_hgnc_id": 11201,
"hgvs_c": "c.613+29G>A",
"hgvs_p": null,
"transcript": "ENST00000396007.6",
"protein_id": "ENSP00000379328.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 377,
"cds_start": -4,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "SOX5",
"gene_hgnc_id": 11201,
"hgvs_c": "c.1741+29G>A",
"hgvs_p": null,
"transcript": "NM_001261415.3",
"protein_id": "NP_001248344.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 753,
"cds_start": -4,
"cds_end": null,
"cds_length": 2262,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7028,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "SOX5",
"gene_hgnc_id": 11201,
"hgvs_c": "c.1741+29G>A",
"hgvs_p": null,
"transcript": "ENST00000545921.5",
"protein_id": "ENSP00000443520.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 753,
"cds_start": -4,
"cds_end": null,
"cds_length": 2262,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "SOX5",
"gene_hgnc_id": 11201,
"hgvs_c": "c.1732+29G>A",
"hgvs_p": null,
"transcript": "NM_152989.5",
"protein_id": "NP_694534.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 750,
"cds_start": -4,
"cds_end": null,
"cds_length": 2253,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "SOX5",
"gene_hgnc_id": 11201,
"hgvs_c": "c.1666+29G>A",
"hgvs_p": null,
"transcript": "NM_001330785.2",
"protein_id": "NP_001317714.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 728,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 6971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "SOX5",
"gene_hgnc_id": 11201,
"hgvs_c": "c.1666+29G>A",
"hgvs_p": null,
"transcript": "ENST00000537393.5",
"protein_id": "ENSP00000439832.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 728,
"cds_start": -4,
"cds_end": null,
"cds_length": 2187,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2769,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "SOX5",
"gene_hgnc_id": 11201,
"hgvs_c": "c.1627+29G>A",
"hgvs_p": null,
"transcript": "ENST00000704299.1",
"protein_id": "ENSP00000515823.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 715,
"cds_start": -4,
"cds_end": null,
"cds_length": 2148,
"cdna_start": null,
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"cdna_length": 2554,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 17,
"intron_rank": 15,
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"gene_symbol": "SOX5",
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"hgvs_c": "c.1408+29G>A",
"hgvs_p": null,
"transcript": "NM_001261414.3",
"protein_id": "NP_001248343.1",
"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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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 17,
"intron_rank": 15,
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"gene_symbol": "SOX5",
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"hgvs_c": "c.1408+29G>A",
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"transcript": "ENST00000646273.1",
"protein_id": "ENSP00000493866.1",
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},
{
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],
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},
{
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],
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"gene_symbol": "SOX5",
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},
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],
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"gene_symbol": "SOX5",
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"hgvs_c": "n.*102+29G>A",
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],
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},
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],
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},
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],
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"gene_symbol": "SOX5",
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"hgvs_c": "c.1963+29G>A",
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"transcript": "XM_047429451.1",
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],
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"hgvs_c": "c.1861+29G>A",
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],
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],
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"gene_symbol": "SOX5",
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},
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],
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"intron_rank": 13,
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"gene_symbol": "SOX5",
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},
{
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},
{
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"gene_symbol": "SOX5",
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},
{
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"intron_variant"
],
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"gene_symbol": "SOX5",
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"hgvs_c": "c.1636+29G>A",
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"transcript": "XM_047429465.1",
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"feature": null
}
],
"gene_symbol": "SOX5",
"gene_hgnc_id": 11201,
"dbsnp": "rs7485662",
"frequency_reference_population": 0.511443,
"hom_count_reference_population": 207987,
"allele_count_reference_population": 807993,
"gnomad_exomes_af": 0.51151,
"gnomad_genomes_af": 0.510815,
"gnomad_exomes_ac": 730389,
"gnomad_genomes_ac": 77604,
"gnomad_exomes_homalt": 188068,
"gnomad_genomes_homalt": 19919,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8999999761581421,
"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": -0.9,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.351,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000451604.7",
"gene_symbol": "SOX5",
"hgnc_id": 11201,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1771+29G>A",
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}
],
"clinvar_disease": "Lamb-Shaffer syndrome,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Lamb-Shaffer syndrome|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}