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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: 2-223776146-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=223776146&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 223776146,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000396654.7",
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "c.183-137G>A",
"hgvs_p": null,
"transcript": "NM_001039569.2",
"protein_id": "NP_001034658.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 154,
"cds_start": -4,
"cds_end": null,
"cds_length": 465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3986,
"mane_select": "ENST00000396654.7",
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "c.183-137G>A",
"hgvs_p": null,
"transcript": "ENST00000396654.7",
"protein_id": "ENSP00000379891.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 154,
"cds_start": -4,
"cds_end": null,
"cds_length": 465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3986,
"mane_select": "NM_001039569.2",
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "c.183-137G>A",
"hgvs_p": null,
"transcript": "ENST00000443700.5",
"protein_id": "ENSP00000397155.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 164,
"cds_start": -4,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1785,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "c.183-137G>A",
"hgvs_p": null,
"transcript": "ENST00000446015.6",
"protein_id": "ENSP00000388738.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 154,
"cds_start": -4,
"cds_end": null,
"cds_length": 465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 499,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.183-137G>A",
"hgvs_p": null,
"transcript": "ENST00000415298.5",
"protein_id": "ENSP00000401705.1",
"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": 2515,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286239",
"gene_hgnc_id": null,
"hgvs_c": "n.*1147-137G>A",
"hgvs_p": null,
"transcript": "ENST00000650969.1",
"protein_id": "ENSP00000498456.1",
"transcript_support_level": null,
"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": 3429,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.195G>A",
"hgvs_p": null,
"transcript": "ENST00000699385.1",
"protein_id": "ENSP00000514349.1",
"transcript_support_level": null,
"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": 1256,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.189G>A",
"hgvs_p": null,
"transcript": "ENST00000699390.1",
"protein_id": "ENSP00000514353.1",
"transcript_support_level": null,
"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": 1115,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.195G>A",
"hgvs_p": null,
"transcript": "ENST00000699391.1",
"protein_id": "ENSP00000514354.1",
"transcript_support_level": null,
"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": 1151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "c.-11G>A",
"hgvs_p": null,
"transcript": "ENST00000444408.1",
"protein_id": "ENSP00000399738.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 55,
"cds_start": -4,
"cds_end": null,
"cds_length": 170,
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "c.183-137G>A",
"hgvs_p": null,
"transcript": "ENST00000409375.1",
"protein_id": "ENSP00000387199.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 137,
"cds_start": -4,
"cds_end": null,
"cds_length": 414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 552,
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "c.183-137G>A",
"hgvs_p": null,
"transcript": "ENST00000699387.1",
"protein_id": "ENSP00000514351.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 137,
"cds_start": -4,
"cds_end": null,
"cds_length": 414,
"cdna_start": null,
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"cdna_length": 2100,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "c.184+1543G>A",
"hgvs_p": null,
"transcript": "ENST00000396653.2",
"protein_id": "ENSP00000379890.2",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 63,
"cds_start": -4,
"cds_end": null,
"cds_length": 192,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.182+1545G>A",
"hgvs_p": null,
"transcript": "ENST00000334271.7",
"protein_id": "ENSP00000333888.3",
"transcript_support_level": 2,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.230-137G>A",
"hgvs_p": null,
"transcript": "ENST00000699384.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 2401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.183-137G>A",
"hgvs_p": null,
"transcript": "ENST00000699386.1",
"protein_id": "ENSP00000514350.1",
"transcript_support_level": null,
"aa_start": null,
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
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"intron_rank": 2,
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"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.182+1545G>A",
"hgvs_p": null,
"transcript": "ENST00000699389.1",
"protein_id": "ENSP00000514352.1",
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"aa_start": null,
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"cds_start": -4,
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"cdna_length": 1211,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.120-137G>A",
"hgvs_p": null,
"transcript": "ENST00000699392.1",
"protein_id": "ENSP00000514355.1",
"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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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.320-137G>A",
"hgvs_p": null,
"transcript": "ENST00000699393.1",
"protein_id": null,
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"feature": null
},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.315-137G>A",
"hgvs_p": null,
"transcript": "NR_110905.2",
"protein_id": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "n.314+1545G>A",
"hgvs_p": null,
"transcript": "NR_110906.2",
"protein_id": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"hgvs_c": "c.183-137G>A",
"hgvs_p": null,
"transcript": "XM_011510600.4",
"protein_id": "XP_011508902.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 108,
"cds_start": -4,
"cds_end": null,
"cds_length": 327,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3848,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AP1S3",
"gene_hgnc_id": 18971,
"dbsnp": "rs11902103",
"frequency_reference_population": 0.100663535,
"hom_count_reference_population": 6540,
"allele_count_reference_population": 72365,
"gnomad_exomes_af": 0.0867709,
"gnomad_genomes_af": 0.152407,
"gnomad_exomes_ac": 49175,
"gnomad_genomes_ac": 23190,
"gnomad_exomes_homalt": 3542,
"gnomad_genomes_homalt": 2998,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8399999737739563,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.18000000715255737,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.84,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.306,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.18,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BA1",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000396654.7",
"gene_symbol": "AP1S3",
"hgnc_id": 18971,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.183-137G>A",
"hgvs_p": null
},
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000650969.1",
"gene_symbol": "ENSG00000286239",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*1147-137G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}