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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-49251440-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=49251440&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 49251440,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000376207.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.1190G>A",
"hgvs_p": "p.Arg397Gln",
"transcript": "NM_014009.4",
"protein_id": "NP_054728.2",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 431,
"cds_start": 1190,
"cds_end": null,
"cds_length": 1296,
"cdna_start": 1262,
"cdna_end": null,
"cdna_length": 2264,
"mane_select": "ENST00000376207.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.1190G>A",
"hgvs_p": "p.Arg397Gln",
"transcript": "ENST00000376207.10",
"protein_id": "ENSP00000365380.4",
"transcript_support_level": 1,
"aa_start": 397,
"aa_end": null,
"aa_length": 431,
"cds_start": 1190,
"cds_end": null,
"cds_length": 1296,
"cdna_start": 1262,
"cdna_end": null,
"cdna_length": 2264,
"mane_select": "NM_014009.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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.1109G>A",
"hgvs_p": "p.Arg370Gln",
"transcript": "ENST00000518685.6",
"protein_id": "ENSP00000428952.2",
"transcript_support_level": 1,
"aa_start": 370,
"aa_end": null,
"aa_length": 404,
"cds_start": 1109,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 1109,
"cdna_end": null,
"cdna_length": 1215,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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.1265G>A",
"hgvs_p": "p.Arg422Gln",
"transcript": "ENST00000557224.6",
"protein_id": "ENSP00000451208.1",
"transcript_support_level": 2,
"aa_start": 422,
"aa_end": null,
"aa_length": 456,
"cds_start": 1265,
"cds_end": null,
"cds_length": 1371,
"cdna_start": 1337,
"cdna_end": null,
"cdna_length": 1443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.1259G>A",
"hgvs_p": "p.Arg420Gln",
"transcript": "ENST00000455775.7",
"protein_id": "ENSP00000396415.3",
"transcript_support_level": 5,
"aa_start": 420,
"aa_end": null,
"aa_length": 454,
"cds_start": 1259,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 1289,
"cdna_end": null,
"cdna_length": 1434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.1085G>A",
"hgvs_p": "p.Arg362Gln",
"transcript": "NM_001114377.2",
"protein_id": "NP_001107849.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 396,
"cds_start": 1085,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1157,
"cdna_end": null,
"cdna_length": 2159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXP3",
"gene_hgnc_id": 6106,
"hgvs_c": "c.1085G>A",
"hgvs_p": "p.Arg362Gln",
"transcript": "ENST00000376199.7",
"protein_id": "ENSP00000365372.2",
"transcript_support_level": 2,
"aa_start": 362,
"aa_end": null,
"aa_length": 396,
"cds_start": 1085,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1247,
"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.1220G>A",
"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": 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.*105G>A",
"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": 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.*105G>A",
"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": "rs1057520529",
"frequency_reference_population": 0.0000018212365,
"hom_count_reference_population": 1,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000182124,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9372754096984863,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.5400000214576721,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": 0.956,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9861,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.7,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.95,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.54,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 13,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 13,
"benign_score": 0,
"pathogenic_score": 13,
"criteria": [
"PM2",
"PM5",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000376207.10",
"gene_symbol": "FOXP3",
"hgnc_id": 6106,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1190G>A",
"hgvs_p": "p.Arg397Gln"
}
],
"clinvar_disease": "FOXP3-related disorder,Insulin-dependent diabetes mellitus secretory diarrhea syndrome,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6 LP:1",
"phenotype_combined": "not provided|Insulin-dependent diabetes mellitus secretory diarrhea syndrome|FOXP3-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}