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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: 5-78116244-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=78116244&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 78116244,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000255194.11",
"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": 27,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1969-10G>A",
"hgvs_p": null,
"transcript": "NM_003664.5",
"protein_id": "NP_003655.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1094,
"cds_start": -4,
"cds_end": null,
"cds_length": 3285,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3980,
"mane_select": "ENST00000255194.11",
"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": 27,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1969-10G>A",
"hgvs_p": null,
"transcript": "ENST00000255194.11",
"protein_id": "ENSP00000255194.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1094,
"cds_start": -4,
"cds_end": null,
"cds_length": 3285,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3980,
"mane_select": "NM_003664.5",
"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": 27,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1822-10G>A",
"hgvs_p": null,
"transcript": "ENST00000519295.7",
"protein_id": "ENSP00000430597.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1045,
"cds_start": -4,
"cds_end": null,
"cds_length": 3138,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 14714,
"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": 26,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1969-10G>A",
"hgvs_p": null,
"transcript": "ENST00000695515.1",
"protein_id": "ENSP00000511978.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1055,
"cds_start": -4,
"cds_end": null,
"cds_length": 3168,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3744,
"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": 28,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1969-10G>A",
"hgvs_p": null,
"transcript": "ENST00000695511.1",
"protein_id": "ENSP00000511974.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1053,
"cds_start": -4,
"cds_end": null,
"cds_length": 3162,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4045,
"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": 28,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1963-10G>A",
"hgvs_p": null,
"transcript": "ENST00000695454.1",
"protein_id": "ENSP00000511922.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1051,
"cds_start": -4,
"cds_end": null,
"cds_length": 3156,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4064,
"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": 27,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1834-10G>A",
"hgvs_p": null,
"transcript": "ENST00000695513.1",
"protein_id": "ENSP00000511976.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1049,
"cds_start": -4,
"cds_end": null,
"cds_length": 3150,
"cdna_start": null,
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"cdna_length": 3973,
"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": 27,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1822-10G>A",
"hgvs_p": null,
"transcript": "NM_001271769.2",
"protein_id": "NP_001258698.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1045,
"cds_start": -4,
"cds_end": null,
"cds_length": 3138,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5796,
"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": 28,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1912-10G>A",
"hgvs_p": null,
"transcript": "ENST00000695453.1",
"protein_id": "ENSP00000511921.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1034,
"cds_start": -4,
"cds_end": null,
"cds_length": 3105,
"cdna_start": null,
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"cdna_length": 3977,
"mane_select": 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,
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"exon_count": 25,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1969-10G>A",
"hgvs_p": null,
"transcript": "ENST00000695512.1",
"protein_id": "ENSP00000511975.1",
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 26,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1969-10G>A",
"hgvs_p": null,
"transcript": "ENST00000695510.1",
"protein_id": "ENSP00000511973.1",
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"cds_start": -4,
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"gene_symbol": "AP3B1",
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},
{
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],
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"gene_symbol": "AP3B1",
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"hgvs_c": "c.1969-10G>A",
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"transcript": "NM_001410752.1",
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},
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],
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"gene_symbol": "AP3B1",
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"hgvs_c": "c.1969-10G>A",
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"transcript": "ENST00000519888.6",
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},
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],
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},
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],
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"gene_symbol": "AP3B1",
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"transcript": "ENST00000695450.1",
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},
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],
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"gene_symbol": "AP3B1",
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"hgvs_c": "n.*145-10G>A",
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"transcript": "ENST00000517561.2",
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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": "AP3B1",
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"hgvs_c": "n.2127-10G>A",
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"transcript": "ENST00000695505.1",
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},
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"strand": false,
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],
"exon_rank": null,
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"intron_rank": 17,
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"gene_symbol": "AP3B1",
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"hgvs_c": "n.1969-10G>A",
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"protein_id": "ENSP00000511970.1",
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"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"dbsnp": "rs77009095",
"frequency_reference_population": 0.069233194,
"hom_count_reference_population": 4256,
"allele_count_reference_population": 110353,
"gnomad_exomes_af": 0.0709428,
"gnomad_genomes_af": 0.0530393,
"gnomad_exomes_ac": 102280,
"gnomad_genomes_ac": 8073,
"gnomad_exomes_homalt": 3930,
"gnomad_genomes_homalt": 326,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6100000143051147,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.15199999511241913,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.179,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000365887800970999,
"dbscsnv_ada_prediction": "Benign",
"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": "ENST00000255194.11",
"gene_symbol": "AP3B1",
"hgnc_id": 566,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1969-10G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Hermansky-Pudlak syndrome,Hermansky-Pudlak syndrome 2,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:4",
"phenotype_combined": "not specified|Hermansky-Pudlak syndrome|not provided|Hermansky-Pudlak syndrome 2",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}