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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: 10-6018094-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=6018094&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 6018094,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_000417.3",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RA",
"gene_hgnc_id": 6008,
"hgvs_c": "c.753C>T",
"hgvs_p": "p.Ile251Ile",
"transcript": "NM_000417.3",
"protein_id": "NP_000408.1",
"transcript_support_level": null,
"aa_start": 251,
"aa_end": null,
"aa_length": 272,
"cds_start": 753,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000379959.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000417.3"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RA",
"gene_hgnc_id": 6008,
"hgvs_c": "c.753C>T",
"hgvs_p": "p.Ile251Ile",
"transcript": "ENST00000379959.8",
"protein_id": "ENSP00000369293.3",
"transcript_support_level": 1,
"aa_start": 251,
"aa_end": null,
"aa_length": 272,
"cds_start": 753,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000417.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379959.8"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RA",
"gene_hgnc_id": 6008,
"hgvs_c": "c.537C>T",
"hgvs_p": "p.Ile179Ile",
"transcript": "ENST00000379954.5",
"protein_id": "ENSP00000369287.1",
"transcript_support_level": 1,
"aa_start": 179,
"aa_end": null,
"aa_length": 200,
"cds_start": 537,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379954.5"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RA",
"gene_hgnc_id": 6008,
"hgvs_c": "c.465C>T",
"hgvs_p": "p.Ile155Ile",
"transcript": "ENST00000447847.2",
"protein_id": "ENSP00000402024.2",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 176,
"cds_start": 465,
"cds_end": null,
"cds_length": 531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000447847.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RA",
"gene_hgnc_id": 6008,
"hgvs_c": "c.726C>T",
"hgvs_p": "p.Ile242Ile",
"transcript": "ENST00000256876.10",
"protein_id": "ENSP00000256876.6",
"transcript_support_level": 5,
"aa_start": 242,
"aa_end": null,
"aa_length": 263,
"cds_start": 726,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000256876.10"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RA",
"gene_hgnc_id": 6008,
"hgvs_c": "c.681C>T",
"hgvs_p": "p.Ile227Ile",
"transcript": "ENST00000697424.1",
"protein_id": "ENSP00000513307.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 248,
"cds_start": 681,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000697424.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RA",
"gene_hgnc_id": 6008,
"hgvs_c": "c.537C>T",
"hgvs_p": "p.Ile179Ile",
"transcript": "NM_001308242.2",
"protein_id": "NP_001295171.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 200,
"cds_start": 537,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308242.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RA",
"gene_hgnc_id": 6008,
"hgvs_c": "c.465C>T",
"hgvs_p": "p.Ile155Ile",
"transcript": "NM_001308243.2",
"protein_id": "NP_001295172.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 176,
"cds_start": 465,
"cds_end": null,
"cds_length": 531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308243.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RA",
"gene_hgnc_id": 6008,
"hgvs_c": "n.568C>T",
"hgvs_p": null,
"transcript": "ENST00000649218.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000649218.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124902368",
"gene_hgnc_id": null,
"hgvs_c": "n.143+1762G>A",
"hgvs_p": null,
"transcript": "XR_007062042.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007062042.1"
}
],
"gene_symbol": "IL2RA",
"gene_hgnc_id": 6008,
"dbsnp": "rs12722698",
"frequency_reference_population": 0.0030676976,
"hom_count_reference_population": 136,
"allele_count_reference_population": 4951,
"gnomad_exomes_af": 0.00163783,
"gnomad_genomes_af": 0.0167976,
"gnomad_exomes_ac": 2394,
"gnomad_genomes_ac": 2557,
"gnomad_exomes_homalt": 65,
"gnomad_genomes_homalt": 71,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7400000095367432,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.74,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.359,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_000417.3",
"gene_symbol": "IL2RA",
"hgnc_id": 6008,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.753C>T",
"hgvs_p": "p.Ile251Ile"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "XR_007062042.1",
"gene_symbol": "LOC124902368",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.143+1762G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Immunodeficiency due to CD25 deficiency,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "Immunodeficiency due to CD25 deficiency|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}