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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: 10-73599700-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=73599700&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 73599700,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "NM_001391941.1",
"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": 20,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "c.-17-24025C>T",
"hgvs_p": null,
"transcript": "ENST00000422491.7",
"protein_id": "ENSP00000407368.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 837,
"cds_start": -4,
"cds_end": null,
"cds_length": 2514,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5688,
"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": 24,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "c.-703-23339C>T",
"hgvs_p": null,
"transcript": "NM_001391941.1",
"protein_id": "NP_001378870.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1706,
"cds_start": -4,
"cds_end": null,
"cds_length": 5121,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6960,
"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": 24,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "c.-243-23339C>T",
"hgvs_p": null,
"transcript": "NM_001391953.1",
"protein_id": "NP_001378882.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1684,
"cds_start": -4,
"cds_end": null,
"cds_length": 5055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6464,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "c.-17-24025C>T",
"hgvs_p": null,
"transcript": "NM_152586.4",
"protein_id": "NP_689799.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1684,
"cds_start": -4,
"cds_end": null,
"cds_length": 5055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6208,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "c.-17-24025C>T",
"hgvs_p": null,
"transcript": "ENST00000339859.8",
"protein_id": "ENSP00000345216.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1684,
"cds_start": -4,
"cds_end": null,
"cds_length": 5055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6247,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "c.-581-23339C>T",
"hgvs_p": null,
"transcript": "ENST00000689425.1",
"protein_id": "ENSP00000508413.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1644,
"cds_start": -4,
"cds_end": null,
"cds_length": 4935,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6776,
"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": 22,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "c.-17-24025C>T",
"hgvs_p": null,
"transcript": "NM_001391949.1",
"protein_id": "NP_001378878.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1637,
"cds_start": -4,
"cds_end": null,
"cds_length": 4914,
"cdna_start": null,
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"cdna_length": 6067,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "c.-581-23339C>T",
"hgvs_p": null,
"transcript": "NM_001391952.1",
"protein_id": "NP_001378881.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1637,
"cds_start": -4,
"cds_end": null,
"cds_length": 4914,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6631,
"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": 22,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "c.-703-23339C>T",
"hgvs_p": null,
"transcript": "NM_001378208.1",
"protein_id": "NP_001365137.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1627,
"cds_start": -4,
"cds_end": null,
"cds_length": 4884,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 1,
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"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "c.-704+1832C>T",
"hgvs_p": null,
"transcript": "NM_001378209.1",
"protein_id": "NP_001365138.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 1627,
"cds_start": -4,
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"cds_length": 4884,
"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,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 1,
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"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "c.-581-23339C>T",
"hgvs_p": null,
"transcript": "NM_001391945.1",
"protein_id": "NP_001378874.1",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
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"exon_count": 23,
"intron_rank": 1,
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"gene_symbol": "USP54",
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"hgvs_c": "c.-243-23339C>T",
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"transcript": "NM_001391946.1",
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},
{
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"strand": false,
"consequences": [
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],
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"intron_rank": 1,
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"gene_symbol": "USP54",
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"hgvs_c": "c.-17-24025C>T",
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"transcript": "NM_001391948.1",
"protein_id": "NP_001378877.1",
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},
{
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"strand": false,
"consequences": [
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],
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"gene_symbol": "USP54",
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"hgvs_c": "c.-581-23339C>T",
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"transcript": "NM_001391954.1",
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},
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],
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"gene_symbol": "USP54",
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"transcript": "NM_001350995.2",
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},
{
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"consequences": [
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],
"exon_rank": null,
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"intron_rank": 1,
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"gene_symbol": "USP54",
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"hgvs_c": "c.-17-24025C>T",
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},
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],
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"transcript": "NM_001391947.1",
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},
{
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"strand": false,
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],
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"intron_rank": 1,
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"gene_symbol": "USP54",
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"hgvs_c": "c.-243-23339C>T",
"hgvs_p": null,
"transcript": "NM_001391950.1",
"protein_id": "NP_001378879.1",
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},
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],
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"intron_rank": 1,
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},
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],
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"transcript": "ENST00000433394.1",
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},
{
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],
"exon_rank": null,
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"intron_rank": 5,
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"gene_symbol": "USP54",
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"hgvs_c": "n.433+11831C>T",
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"transcript": "ENST00000474929.1",
"protein_id": null,
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 24,
"intron_rank": 1,
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"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"hgvs_c": "n.-581-23339C>T",
"hgvs_p": null,
"transcript": "ENST00000685297.1",
"protein_id": "ENSP00000508456.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"mane_select": null,
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"biotype": null,
"feature": null
}
],
"gene_symbol": "USP54",
"gene_hgnc_id": 23513,
"dbsnp": "rs16930750",
"frequency_reference_population": 0.051133674,
"hom_count_reference_population": 604,
"allele_count_reference_population": 7776,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0511337,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 7776,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 604,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9200000166893005,
"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": -0.92,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.211,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001391941.1",
"gene_symbol": "USP54",
"hgnc_id": 23513,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.-703-23339C>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}