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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: 9-116687354-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=116687354&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 116687354,
"ref": "T",
"alt": "C",
"effect": "5_prime_UTR_variant",
"transcript": "NM_012210.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM32",
"gene_hgnc_id": 16380,
"hgvs_c": "c.-109T>C",
"hgvs_p": null,
"transcript": "NM_012210.4",
"protein_id": "NP_036342.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 653,
"cds_start": -4,
"cds_end": null,
"cds_length": 1962,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3715,
"mane_select": "ENST00000450136.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM32",
"gene_hgnc_id": 16380,
"hgvs_c": "c.-109T>C",
"hgvs_p": null,
"transcript": "ENST00000450136.2",
"protein_id": "ENSP00000408292.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 653,
"cds_start": -4,
"cds_end": null,
"cds_length": 1962,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3715,
"mane_select": "NM_012210.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM32",
"gene_hgnc_id": 16380,
"hgvs_c": "c.-106T>C",
"hgvs_p": null,
"transcript": "ENST00000373983.2",
"protein_id": "ENSP00000363095.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 653,
"cds_start": -4,
"cds_end": null,
"cds_length": 1962,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3688,
"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": 23,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "ASTN2",
"gene_hgnc_id": 17021,
"hgvs_c": "c.2807-35561A>G",
"hgvs_p": null,
"transcript": "NM_001365068.1",
"protein_id": "NP_001351997.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1339,
"cds_start": -4,
"cds_end": null,
"cds_length": 4020,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6878,
"mane_select": "ENST00000313400.9",
"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": 23,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "ASTN2",
"gene_hgnc_id": 17021,
"hgvs_c": "c.2807-35561A>G",
"hgvs_p": null,
"transcript": "ENST00000313400.9",
"protein_id": "ENSP00000314038.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1339,
"cds_start": -4,
"cds_end": null,
"cds_length": 4020,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6878,
"mane_select": "NM_001365068.1",
"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": 22,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "ASTN2",
"gene_hgnc_id": 17021,
"hgvs_c": "c.2654-35561A>G",
"hgvs_p": null,
"transcript": "ENST00000361209.6",
"protein_id": "ENSP00000354504.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1288,
"cds_start": -4,
"cds_end": null,
"cds_length": 3867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4622,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM32",
"gene_hgnc_id": 16380,
"hgvs_c": "c.-106T>C",
"hgvs_p": null,
"transcript": "NM_001099679.2",
"protein_id": "NP_001093149.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 653,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 3712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM32",
"gene_hgnc_id": 16380,
"hgvs_c": "c.-170T>C",
"hgvs_p": null,
"transcript": "NM_001379048.1",
"protein_id": "NP_001365977.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 653,
"cds_start": -4,
"cds_end": null,
"cds_length": 1962,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3776,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM32",
"gene_hgnc_id": 16380,
"hgvs_c": "c.-170T>C",
"hgvs_p": null,
"transcript": "ENST00000411410.1",
"protein_id": "ENSP00000412603.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 171,
"cds_start": -4,
"cds_end": null,
"cds_length": 518,
"cdna_start": null,
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"cdna_length": 699,
"mane_select": null,
"mane_plus": 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": 23,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "ASTN2",
"gene_hgnc_id": 17021,
"hgvs_c": "c.2795-35561A>G",
"hgvs_p": null,
"transcript": "NM_001365069.1",
"protein_id": "NP_001351998.1",
"transcript_support_level": null,
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"cds_start": -4,
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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": 23,
"intron_rank": 15,
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"gene_symbol": "ASTN2",
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"hgvs_c": "c.2654-35561A>G",
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"transcript": "ENST00000361477.8",
"protein_id": "ENSP00000355116.5",
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},
{
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],
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},
{
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],
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"gene_symbol": "ASTN2",
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"transcript": "ENST00000373986.7",
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},
{
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],
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"intron_rank": null,
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},
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],
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},
{
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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": "TRIM32",
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"hgvs_c": "c.-390T>C",
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},
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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,
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],
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"gene_symbol": "ASTN2",
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"hgvs_c": "c.-327A>G",
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"transcript": "NM_001184734.1",
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},
{
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],
"exon_rank": null,
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"exon_count": 5,
"intron_rank": null,
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"gene_symbol": "ASTN2",
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"hgvs_c": "c.-327A>G",
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"transcript": "NM_001184735.1",
"protein_id": "NP_001171664.1",
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TRIM32",
"gene_hgnc_id": 16380,
"dbsnp": "rs886063378",
"frequency_reference_population": 0.00042810538,
"hom_count_reference_population": 1,
"allele_count_reference_population": 316,
"gnomad_exomes_af": 0.000449005,
"gnomad_genomes_af": 0.000336243,
"gnomad_exomes_ac": 270,
"gnomad_genomes_ac": 46,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5899999737739563,
"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": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.161,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_012210.4",
"gene_symbol": "TRIM32",
"hgnc_id": 16380,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-109T>C",
"hgvs_p": null
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001365068.1",
"gene_symbol": "ASTN2",
"hgnc_id": 17021,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2807-35561A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Bardet-Biedl syndrome 11,Sarcotubular myopathy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Bardet-Biedl syndrome 11|Sarcotubular myopathy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}