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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-49251711-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=49251711&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 49251711,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000376207.10",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.1099T>C",
"hgvs_p": "p.Phe367Leu",
"transcript": "NM_014009.4",
"protein_id": "NP_054728.2",
"transcript_support_level": null,
"aa_start": 367,
"aa_end": null,
"aa_length": 431,
"cds_start": 1099,
"cds_end": null,
"cds_length": 1296,
"cdna_start": 1171,
"cdna_end": null,
"cdna_length": 2264,
"mane_select": "ENST00000376207.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.1099T>C",
"hgvs_p": "p.Phe367Leu",
"transcript": "ENST00000376207.10",
"protein_id": "ENSP00000365380.4",
"transcript_support_level": 1,
"aa_start": 367,
"aa_end": null,
"aa_length": 431,
"cds_start": 1099,
"cds_end": null,
"cds_length": 1296,
"cdna_start": 1171,
"cdna_end": null,
"cdna_length": 2264,
"mane_select": "NM_014009.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.1018T>C",
"hgvs_p": "p.Phe340Leu",
"transcript": "ENST00000518685.6",
"protein_id": "ENSP00000428952.2",
"transcript_support_level": 1,
"aa_start": 340,
"aa_end": null,
"aa_length": 404,
"cds_start": 1018,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 1018,
"cdna_end": null,
"cdna_length": 1215,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.994T>C",
"hgvs_p": "p.Phe332Leu",
"transcript": "ENST00000557224.6",
"protein_id": "ENSP00000451208.1",
"transcript_support_level": 2,
"aa_start": 332,
"aa_end": null,
"aa_length": 456,
"cds_start": 994,
"cds_end": null,
"cds_length": 1371,
"cdna_start": 1066,
"cdna_end": null,
"cdna_length": 1443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.1168T>C",
"hgvs_p": "p.Phe390Leu",
"transcript": "ENST00000455775.7",
"protein_id": "ENSP00000396415.3",
"transcript_support_level": 5,
"aa_start": 390,
"aa_end": null,
"aa_length": 454,
"cds_start": 1168,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 1198,
"cdna_end": null,
"cdna_length": 1434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.994T>C",
"hgvs_p": "p.Phe332Leu",
"transcript": "NM_001114377.2",
"protein_id": "NP_001107849.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 396,
"cds_start": 994,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1066,
"cdna_end": null,
"cdna_length": 2159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.994T>C",
"hgvs_p": "p.Phe332Leu",
"transcript": "ENST00000376199.7",
"protein_id": "ENSP00000365372.2",
"transcript_support_level": 2,
"aa_start": 332,
"aa_end": null,
"aa_length": 396,
"cds_start": 994,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1156,
"cdna_end": null,
"cdna_length": 1597,
"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": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "n.949T>C",
"hgvs_p": null,
"transcript": "ENST00000376197.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 1326,
"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": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "n.*14T>C",
"hgvs_p": null,
"transcript": "ENST00000651307.1",
"protein_id": "ENSP00000498454.1",
"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": 1297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "n.*14T>C",
"hgvs_p": null,
"transcript": "ENST00000651307.1",
"protein_id": "ENSP00000498454.1",
"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": 1297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"dbsnp": "rs122467175",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9231762886047363,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.758,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.999,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.31,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.214,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.11,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM1",
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000376207.10",
"gene_symbol": "FOXP3",
"hgnc_id": 6106,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1099T>C",
"hgvs_p": "p.Phe367Leu"
}
],
"clinvar_disease": "Insulin-dependent diabetes mellitus secretory diarrhea syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Insulin-dependent diabetes mellitus secretory diarrhea syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}