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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: 20-49908290-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=49908290&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 49908290,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "ENST00000289431.10",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA2",
"gene_hgnc_id": 14681,
"hgvs_c": "c.201T>C",
"hgvs_p": "p.Tyr67Tyr",
"transcript": "NM_006038.4",
"protein_id": "NP_006029.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 520,
"cds_start": 201,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 453,
"cdna_end": null,
"cdna_length": 4043,
"mane_select": "ENST00000289431.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA2",
"gene_hgnc_id": 14681,
"hgvs_c": "c.201T>C",
"hgvs_p": "p.Tyr67Tyr",
"transcript": "ENST00000289431.10",
"protein_id": "ENSP00000289431.5",
"transcript_support_level": 1,
"aa_start": 67,
"aa_end": null,
"aa_length": 520,
"cds_start": 201,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 453,
"cdna_end": null,
"cdna_length": 4043,
"mane_select": "NM_006038.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA2",
"gene_hgnc_id": 14681,
"hgvs_c": "c.201T>C",
"hgvs_p": "p.Tyr67Tyr",
"transcript": "NM_001135773.2",
"protein_id": "NP_001129245.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 520,
"cds_start": 201,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 514,
"cdna_end": null,
"cdna_length": 4104,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA2",
"gene_hgnc_id": 14681,
"hgvs_c": "c.201T>C",
"hgvs_p": "p.Tyr67Tyr",
"transcript": "ENST00000422556.1",
"protein_id": "ENSP00000416799.1",
"transcript_support_level": 2,
"aa_start": 67,
"aa_end": null,
"aa_length": 520,
"cds_start": 201,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 551,
"cdna_end": null,
"cdna_length": 4138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA2",
"gene_hgnc_id": 14681,
"hgvs_c": "c.201T>C",
"hgvs_p": "p.Tyr67Tyr",
"transcript": "XM_006723894.2",
"protein_id": "XP_006723957.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 520,
"cds_start": 201,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 578,
"cdna_end": null,
"cdna_length": 4168,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA2",
"gene_hgnc_id": 14681,
"hgvs_c": "c.201T>C",
"hgvs_p": "p.Tyr67Tyr",
"transcript": "XM_047440623.1",
"protein_id": "XP_047296579.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 520,
"cds_start": 201,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 2813,
"cdna_end": null,
"cdna_length": 6403,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA2",
"gene_hgnc_id": 14681,
"hgvs_c": "c.201T>C",
"hgvs_p": "p.Tyr67Tyr",
"transcript": "XM_047440624.1",
"protein_id": "XP_047296580.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 520,
"cds_start": 201,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 803,
"cdna_end": null,
"cdna_length": 4393,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPATA2",
"gene_hgnc_id": 14681,
"dbsnp": "rs2769982",
"frequency_reference_population": 0.4841437,
"hom_count_reference_population": 197571,
"allele_count_reference_population": 781436,
"gnomad_exomes_af": 0.490619,
"gnomad_genomes_af": 0.421955,
"gnomad_exomes_ac": 717206,
"gnomad_genomes_ac": 64230,
"gnomad_exomes_homalt": 181928,
"gnomad_genomes_homalt": 15643,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7799999713897705,
"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": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.235,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000289431.10",
"gene_symbol": "SPATA2",
"hgnc_id": 14681,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.201T>C",
"hgvs_p": "p.Tyr67Tyr"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}