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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: 4-184010535-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=184010535&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 184010535,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000308497.9",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX2",
"gene_hgnc_id": 25450,
"hgvs_c": "c.1697C>A",
"hgvs_p": "p.Pro566Gln",
"transcript": "NM_020225.3",
"protein_id": "NP_064610.1",
"transcript_support_level": null,
"aa_start": 566,
"aa_end": null,
"aa_length": 926,
"cds_start": 1697,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 3181,
"cdna_end": null,
"cdna_length": 10507,
"mane_select": "ENST00000308497.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX2",
"gene_hgnc_id": 25450,
"hgvs_c": "c.1697C>A",
"hgvs_p": "p.Pro566Gln",
"transcript": "ENST00000308497.9",
"protein_id": "ENSP00000311257.4",
"transcript_support_level": 1,
"aa_start": 566,
"aa_end": null,
"aa_length": 926,
"cds_start": 1697,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 3181,
"cdna_end": null,
"cdna_length": 10507,
"mane_select": "NM_020225.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX2",
"gene_hgnc_id": 25450,
"hgvs_c": "c.1565C>A",
"hgvs_p": "p.Pro522Gln",
"transcript": "XM_047415989.1",
"protein_id": "XP_047271945.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 882,
"cds_start": 1565,
"cds_end": null,
"cds_length": 2649,
"cdna_start": 13559,
"cdna_end": null,
"cdna_length": 20885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX2",
"gene_hgnc_id": 25450,
"hgvs_c": "c.1559C>A",
"hgvs_p": "p.Pro520Gln",
"transcript": "XM_011532131.2",
"protein_id": "XP_011530433.1",
"transcript_support_level": null,
"aa_start": 520,
"aa_end": null,
"aa_length": 880,
"cds_start": 1559,
"cds_end": null,
"cds_length": 2643,
"cdna_start": 2406,
"cdna_end": null,
"cdna_length": 9732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX2",
"gene_hgnc_id": 25450,
"hgvs_c": "c.1556C>A",
"hgvs_p": "p.Pro519Gln",
"transcript": "XM_017008467.2",
"protein_id": "XP_016863956.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 879,
"cds_start": 1556,
"cds_end": null,
"cds_length": 2640,
"cdna_start": 1976,
"cdna_end": null,
"cdna_length": 9302,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX2",
"gene_hgnc_id": 25450,
"hgvs_c": "c.1556C>A",
"hgvs_p": "p.Pro519Gln",
"transcript": "XM_047415990.1",
"protein_id": "XP_047271946.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 879,
"cds_start": 1556,
"cds_end": null,
"cds_length": 2640,
"cdna_start": 2239,
"cdna_end": null,
"cdna_length": 9565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX2",
"gene_hgnc_id": 25450,
"hgvs_c": "c.1511C>A",
"hgvs_p": "p.Pro504Gln",
"transcript": "XM_024454157.2",
"protein_id": "XP_024309925.1",
"transcript_support_level": null,
"aa_start": 504,
"aa_end": null,
"aa_length": 864,
"cds_start": 1511,
"cds_end": null,
"cds_length": 2595,
"cdna_start": 1803,
"cdna_end": null,
"cdna_length": 9129,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX2",
"gene_hgnc_id": 25450,
"hgvs_c": "c.1511C>A",
"hgvs_p": "p.Pro504Gln",
"transcript": "XM_017008466.2",
"protein_id": "XP_016863955.2",
"transcript_support_level": null,
"aa_start": 504,
"aa_end": null,
"aa_length": 800,
"cds_start": 1511,
"cds_end": null,
"cds_length": 2403,
"cdna_start": 1565,
"cdna_end": null,
"cdna_length": 2457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "STOX2",
"gene_hgnc_id": 25450,
"hgvs_c": "c.518-6554C>A",
"hgvs_p": null,
"transcript": "ENST00000513034.3",
"protein_id": "ENSP00000422118.3",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 195,
"cds_start": -4,
"cds_end": null,
"cds_length": 588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "STOX2",
"gene_hgnc_id": 25450,
"hgvs_c": "n.188-6554C>A",
"hgvs_p": null,
"transcript": "NR_132761.1",
"protein_id": null,
"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": 6629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX2",
"gene_hgnc_id": 25450,
"hgvs_c": "c.-239C>A",
"hgvs_p": null,
"transcript": "ENST00000506529.1",
"protein_id": "ENSP00000426209.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 218,
"cds_start": -4,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "STOX2",
"gene_hgnc_id": 25450,
"dbsnp": "rs199563171",
"frequency_reference_population": 0.0000013684328,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136843,
"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": 0.03732690215110779,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.07,
"revel_prediction": "Benign",
"alphamissense_score": 0.0936,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.343,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000308497.9",
"gene_symbol": "STOX2",
"hgnc_id": 25450,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1697C>A",
"hgvs_p": "p.Pro566Gln"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}