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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: 20-22581940-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=22581940&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 22581940,
"ref": "C",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_021784.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXA2",
"gene_hgnc_id": 5022,
"hgvs_c": "c.1302G>C",
"hgvs_p": "p.Thr434Thr",
"transcript": "NM_021784.5",
"protein_id": "NP_068556.2",
"transcript_support_level": null,
"aa_start": 434,
"aa_end": null,
"aa_length": 463,
"cds_start": 1302,
"cds_end": null,
"cds_length": 1392,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000419308.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_021784.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXA2",
"gene_hgnc_id": 5022,
"hgvs_c": "c.1302G>C",
"hgvs_p": "p.Thr434Thr",
"transcript": "ENST00000419308.7",
"protein_id": "ENSP00000400341.3",
"transcript_support_level": 1,
"aa_start": 434,
"aa_end": null,
"aa_length": 463,
"cds_start": 1302,
"cds_end": null,
"cds_length": 1392,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_021784.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000419308.7"
},
{
"aa_ref": "T",
"aa_alt": "T",
"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": "FOXA2",
"gene_hgnc_id": 5022,
"hgvs_c": "c.1284G>C",
"hgvs_p": "p.Thr428Thr",
"transcript": "ENST00000377115.4",
"protein_id": "ENSP00000366319.4",
"transcript_support_level": 1,
"aa_start": 428,
"aa_end": null,
"aa_length": 457,
"cds_start": 1284,
"cds_end": null,
"cds_length": 1374,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000377115.4"
},
{
"aa_ref": "T",
"aa_alt": "T",
"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": "FOXA2",
"gene_hgnc_id": 5022,
"hgvs_c": "c.1284G>C",
"hgvs_p": "p.Thr428Thr",
"transcript": "NM_153675.3",
"protein_id": "NP_710141.1",
"transcript_support_level": null,
"aa_start": 428,
"aa_end": null,
"aa_length": 457,
"cds_start": 1284,
"cds_end": null,
"cds_length": 1374,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_153675.3"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXA2",
"gene_hgnc_id": 5022,
"hgvs_c": "c.777G>C",
"hgvs_p": "p.Thr259Thr",
"transcript": "ENST00000938926.1",
"protein_id": "ENSP00000608985.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 288,
"cds_start": 777,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938926.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"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": "FOXA2",
"gene_hgnc_id": 5022,
"hgvs_c": "c.1284G>C",
"hgvs_p": "p.Thr428Thr",
"transcript": "XM_047440133.1",
"protein_id": "XP_047296089.1",
"transcript_support_level": null,
"aa_start": 428,
"aa_end": null,
"aa_length": 457,
"cds_start": 1284,
"cds_end": null,
"cds_length": 1374,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047440133.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXA2",
"gene_hgnc_id": 5022,
"hgvs_c": "c.1194G>C",
"hgvs_p": "p.Thr398Thr",
"transcript": "XM_047440134.1",
"protein_id": "XP_047296090.1",
"transcript_support_level": null,
"aa_start": 398,
"aa_end": null,
"aa_length": 427,
"cds_start": 1194,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047440134.1"
}
],
"gene_symbol": "FOXA2",
"gene_hgnc_id": 5022,
"dbsnp": "rs201077294",
"frequency_reference_population": 0.000040959392,
"hom_count_reference_population": 0,
"allele_count_reference_population": 66,
"gnomad_exomes_af": 0.0000411216,
"gnomad_genomes_af": 0.0000394052,
"gnomad_exomes_ac": 60,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5299999713897705,
"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": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.123,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_021784.5",
"gene_symbol": "FOXA2",
"hgnc_id": 5022,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1302G>C",
"hgvs_p": "p.Thr434Thr"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}