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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: X-54446073-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=54446073&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"3_prime_UTR_variant"
],
"gene_symbol": "FGD1",
"hgnc_id": 3663,
"hgvs_c": "c.*36C>T",
"hgvs_p": null,
"inheritance_mode": "AD,XL",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_004463.3",
"verdict": "Benign"
},
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"3_prime_UTR_variant"
],
"gene_symbol": "TSR2",
"hgnc_id": 25455,
"hgvs_c": "c.*1523G>A",
"hgvs_p": null,
"inheritance_mode": "AD,XL",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_058163.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_score": -20,
"allele_count_reference_population": 108783,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"chr": "X",
"clinvar_classification": "Benign",
"clinvar_disease": "Aarskog syndrome,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6200000047683716,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 961,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4343,
"cdna_start": null,
"cds_end": null,
"cds_length": 2886,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_004463.3",
"gene_hgnc_id": 3663,
"gene_symbol": "FGD1",
"hgvs_c": "c.*36C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000375135.4",
"protein_coding": true,
"protein_id": "NP_004454.2",
"strand": false,
"transcript": "NM_004463.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 961,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4343,
"cdna_start": null,
"cds_end": null,
"cds_length": 2886,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000375135.4",
"gene_hgnc_id": 3663,
"gene_symbol": "FGD1",
"hgvs_c": "c.*36C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004463.3",
"protein_coding": true,
"protein_id": "ENSP00000364277.3",
"strand": false,
"transcript": "ENST00000375135.4",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 191,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4076,
"cdna_start": null,
"cds_end": null,
"cds_length": 576,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_058163.3",
"gene_hgnc_id": 25455,
"gene_symbol": "TSR2",
"hgvs_c": "c.*1523G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000375151.5",
"protein_coding": true,
"protein_id": "NP_477511.1",
"strand": true,
"transcript": "NM_058163.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 191,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4076,
"cdna_start": null,
"cds_end": null,
"cds_length": 576,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000375151.5",
"gene_hgnc_id": 25455,
"gene_symbol": "TSR2",
"hgvs_c": "c.*1523G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_058163.3",
"protein_coding": true,
"protein_id": "ENSP00000364293.4",
"strand": true,
"transcript": "ENST00000375151.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 961,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4030,
"cdna_start": null,
"cds_end": null,
"cds_length": 2886,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000934021.1",
"gene_hgnc_id": 3663,
"gene_symbol": "FGD1",
"hgvs_c": "c.*36C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604080.1",
"strand": false,
"transcript": "ENST00000934021.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 960,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4328,
"cdna_start": null,
"cds_end": null,
"cds_length": 2883,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000934019.1",
"gene_hgnc_id": 3663,
"gene_symbol": "FGD1",
"hgvs_c": "c.*36C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604078.1",
"strand": false,
"transcript": "ENST00000934019.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 959,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4242,
"cdna_start": null,
"cds_end": null,
"cds_length": 2880,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000934020.1",
"gene_hgnc_id": 3663,
"gene_symbol": "FGD1",
"hgvs_c": "c.*36C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604079.1",
"strand": false,
"transcript": "ENST00000934020.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 907,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3727,
"cdna_start": null,
"cds_end": null,
"cds_length": 2724,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000934022.1",
"gene_hgnc_id": 3663,
"gene_symbol": "FGD1",
"hgvs_c": "c.*36C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604081.1",
"strand": false,
"transcript": "ENST00000934022.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 188,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4067,
"cdna_start": null,
"cds_end": null,
"cds_length": 567,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001346789.2",
"gene_hgnc_id": 25455,
"gene_symbol": "TSR2",
"hgvs_c": "c.*1523G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001333718.1",
"strand": true,
"transcript": "NM_001346789.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 96,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4178,
"cdna_start": null,
"cds_end": null,
"cds_length": 291,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001346790.2",
"gene_hgnc_id": 25455,
"gene_symbol": "TSR2",
"hgvs_c": "c.*1523G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001333719.1",
"strand": true,
"transcript": "NM_001346790.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 96,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4187,
"cdna_start": null,
"cds_end": null,
"cds_length": 291,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001346791.2",
"gene_hgnc_id": 25455,
"gene_symbol": "TSR2",
"hgvs_c": "c.*1523G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001333720.1",
"strand": true,
"transcript": "NM_001346791.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 96,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3985,
"cdna_start": null,
"cds_end": null,
"cds_length": 291,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001346792.2",
"gene_hgnc_id": 25455,
"gene_symbol": "TSR2",
"hgvs_c": "c.*1523G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001333721.1",
"strand": true,
"transcript": "NM_001346792.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs2230265",
"effect": "3_prime_UTR_variant",
"frequency_reference_population": 0.09729769,
"gene_hgnc_id": 3663,
"gene_symbol": "FGD1",
"gnomad_exomes_ac": 99176,
"gnomad_exomes_af": 0.0985011,
"gnomad_exomes_homalt": 5968,
"gnomad_genomes_ac": 9607,
"gnomad_genomes_af": 0.0864009,
"gnomad_genomes_homalt": 597,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 40411,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|not provided|Aarskog syndrome",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.295,
"pos": 54446073,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004463.3"
}
]
}