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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: 11-125893851-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=125893851&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 125893851,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000227474.8",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS3",
"gene_hgnc_id": 25461,
"hgvs_c": "c.1380G>A",
"hgvs_p": "p.Glu460Glu",
"transcript": "NM_031307.4",
"protein_id": "NP_112597.4",
"transcript_support_level": null,
"aa_start": 460,
"aa_end": null,
"aa_length": 481,
"cds_start": 1380,
"cds_end": null,
"cds_length": 1446,
"cdna_start": 1463,
"cdna_end": null,
"cdna_length": 1829,
"mane_select": "ENST00000227474.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS3",
"gene_hgnc_id": 25461,
"hgvs_c": "c.1380G>A",
"hgvs_p": "p.Glu460Glu",
"transcript": "ENST00000227474.8",
"protein_id": "ENSP00000227474.3",
"transcript_support_level": 1,
"aa_start": 460,
"aa_end": null,
"aa_length": 481,
"cds_start": 1380,
"cds_end": null,
"cds_length": 1446,
"cdna_start": 1463,
"cdna_end": null,
"cdna_length": 1829,
"mane_select": "NM_031307.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS3",
"gene_hgnc_id": 25461,
"hgvs_c": "c.1380G>A",
"hgvs_p": "p.Glu460Glu",
"transcript": "ENST00000530811.5",
"protein_id": "ENSP00000432386.1",
"transcript_support_level": 1,
"aa_start": 460,
"aa_end": null,
"aa_length": 481,
"cds_start": 1380,
"cds_end": null,
"cds_length": 1446,
"cdna_start": 1426,
"cdna_end": null,
"cdna_length": 1792,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HYLS1",
"gene_hgnc_id": 26558,
"hgvs_c": "c.-26+2379C>T",
"hgvs_p": null,
"transcript": "NM_001134793.2",
"protein_id": "NP_001128265.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1451,
"mane_select": "ENST00000425380.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HYLS1",
"gene_hgnc_id": 26558,
"hgvs_c": "c.-26+2379C>T",
"hgvs_p": null,
"transcript": "ENST00000425380.7",
"protein_id": "ENSP00000414884.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1451,
"mane_select": "NM_001134793.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS3",
"gene_hgnc_id": 25461,
"hgvs_c": "c.1380G>A",
"hgvs_p": "p.Glu460Glu",
"transcript": "NM_001441237.1",
"protein_id": "NP_001428166.1",
"transcript_support_level": null,
"aa_start": 460,
"aa_end": null,
"aa_length": 481,
"cds_start": 1380,
"cds_end": null,
"cds_length": 1446,
"cdna_start": 1629,
"cdna_end": null,
"cdna_length": 1995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS3",
"gene_hgnc_id": 25461,
"hgvs_c": "c.756G>A",
"hgvs_p": "p.Glu252Glu",
"transcript": "NM_001271985.2",
"protein_id": "NP_001258914.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 273,
"cds_start": 756,
"cds_end": null,
"cds_length": 822,
"cdna_start": 1039,
"cdna_end": null,
"cdna_length": 1405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS3",
"gene_hgnc_id": 25461,
"hgvs_c": "c.756G>A",
"hgvs_p": "p.Glu252Glu",
"transcript": "NM_001441238.1",
"protein_id": "NP_001428167.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 273,
"cds_start": 756,
"cds_end": null,
"cds_length": 822,
"cdna_start": 1205,
"cdna_end": null,
"cdna_length": 1571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS3",
"gene_hgnc_id": 25461,
"hgvs_c": "c.756G>A",
"hgvs_p": "p.Glu252Glu",
"transcript": "ENST00000613398.4",
"protein_id": "ENSP00000481536.1",
"transcript_support_level": 2,
"aa_start": 252,
"aa_end": null,
"aa_length": 273,
"cds_start": 756,
"cds_end": null,
"cds_length": 822,
"cdna_start": 1054,
"cdna_end": null,
"cdna_length": 1419,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS3",
"gene_hgnc_id": 25461,
"hgvs_c": "c.*403G>A",
"hgvs_p": null,
"transcript": "NM_001441239.1",
"protein_id": "NP_001428168.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 176,
"cds_start": -4,
"cds_end": null,
"cds_length": 531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS3",
"gene_hgnc_id": 25461,
"hgvs_c": "c.*403G>A",
"hgvs_p": null,
"transcript": "NM_001441240.1",
"protein_id": "NP_001428169.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 176,
"cds_start": -4,
"cds_end": null,
"cds_length": 531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS3",
"gene_hgnc_id": 25461,
"hgvs_c": "c.*403G>A",
"hgvs_p": null,
"transcript": "NM_001441241.1",
"protein_id": "NP_001428170.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 136,
"cds_start": -4,
"cds_end": null,
"cds_length": 411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1263,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HYLS1",
"gene_hgnc_id": 26558,
"hgvs_c": "c.-25-5493C>T",
"hgvs_p": null,
"transcript": "NM_001377269.1",
"protein_id": "NP_001364198.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HYLS1",
"gene_hgnc_id": 26558,
"hgvs_c": "c.-22-5496C>T",
"hgvs_p": null,
"transcript": "NM_001377270.1",
"protein_id": "NP_001364199.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HYLS1",
"gene_hgnc_id": 26558,
"hgvs_c": "c.-23+2379C>T",
"hgvs_p": null,
"transcript": "NM_001424364.1",
"protein_id": "NP_001411293.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1448,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HYLS1",
"gene_hgnc_id": 26558,
"hgvs_c": "c.-81+2379C>T",
"hgvs_p": null,
"transcript": "NM_145014.3",
"protein_id": "NP_659451.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HYLS1",
"gene_hgnc_id": 26558,
"hgvs_c": "c.-81+2379C>T",
"hgvs_p": null,
"transcript": "ENST00000356438.7",
"protein_id": "ENSP00000348815.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HYLS1",
"gene_hgnc_id": 26558,
"hgvs_c": "c.-26+2379C>T",
"hgvs_p": null,
"transcript": "ENST00000526028.1",
"protein_id": "ENSP00000436833.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1803,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PUS3",
"gene_hgnc_id": 25461,
"dbsnp": "rs3088241",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 0,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.75,
"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": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.008,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000227474.8",
"gene_symbol": "PUS3",
"hgnc_id": 25461,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1380G>A",
"hgvs_p": "p.Glu460Glu"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000425380.7",
"gene_symbol": "HYLS1",
"hgnc_id": 26558,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-26+2379C>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
}