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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: 15-92438444-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=92438444&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ST8SIA2",
"hgnc_id": 10870,
"hgvs_c": "c.382G>A",
"hgvs_p": "p.Asp128Asn",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_006011.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 84,
"alphamissense_prediction": null,
"alphamissense_score": 0.8333,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.53,
"chr": "15",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.1604817509651184,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 375,
"aa_ref": "D",
"aa_start": 128,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5655,
"cdna_start": 566,
"cds_end": null,
"cds_length": 1128,
"cds_start": 382,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_006011.4",
"gene_hgnc_id": 10870,
"gene_symbol": "ST8SIA2",
"hgvs_c": "c.382G>A",
"hgvs_p": "p.Asp128Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000268164.8",
"protein_coding": true,
"protein_id": "NP_006002.1",
"strand": true,
"transcript": "NM_006011.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 375,
"aa_ref": "D",
"aa_start": 128,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5655,
"cdna_start": 566,
"cds_end": null,
"cds_length": 1128,
"cds_start": 382,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000268164.8",
"gene_hgnc_id": 10870,
"gene_symbol": "ST8SIA2",
"hgvs_c": "c.382G>A",
"hgvs_p": "p.Asp128Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006011.4",
"protein_coding": true,
"protein_id": "ENSP00000268164.3",
"strand": true,
"transcript": "ENST00000268164.8",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 354,
"aa_ref": "D",
"aa_start": 107,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1089,
"cdna_start": 343,
"cds_end": null,
"cds_length": 1065,
"cds_start": 319,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000539113.5",
"gene_hgnc_id": 10870,
"gene_symbol": "ST8SIA2",
"hgvs_c": "c.319G>A",
"hgvs_p": "p.Asp107Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000437382.1",
"strand": true,
"transcript": "ENST00000539113.5",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 415,
"aa_ref": "D",
"aa_start": 168,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3264,
"cdna_start": 667,
"cds_end": null,
"cds_length": 1248,
"cds_start": 502,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000957924.1",
"gene_hgnc_id": 10870,
"gene_symbol": "ST8SIA2",
"hgvs_c": "c.502G>A",
"hgvs_p": "p.Asp168Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627983.1",
"strand": true,
"transcript": "ENST00000957924.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 354,
"aa_ref": "D",
"aa_start": 107,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5592,
"cdna_start": 503,
"cds_end": null,
"cds_length": 1065,
"cds_start": 319,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001330416.2",
"gene_hgnc_id": 10870,
"gene_symbol": "ST8SIA2",
"hgvs_c": "c.319G>A",
"hgvs_p": "p.Asp107Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317345.1",
"strand": true,
"transcript": "NM_001330416.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 331,
"aa_ref": "D",
"aa_start": 85,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 998,
"cdna_start": 253,
"cds_end": null,
"cds_length": 998,
"cds_start": 253,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000555434.1",
"gene_hgnc_id": 10870,
"gene_symbol": "ST8SIA2",
"hgvs_c": "c.253G>A",
"hgvs_p": "p.Asp85Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000450851.1",
"strand": true,
"transcript": "ENST00000555434.1",
"transcript_support_level": 5
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 396,
"aa_ref": "D",
"aa_start": 149,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9923,
"cdna_start": 4834,
"cds_end": null,
"cds_length": 1191,
"cds_start": 445,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017022642.2",
"gene_hgnc_id": 10870,
"gene_symbol": "ST8SIA2",
"hgvs_c": "c.445G>A",
"hgvs_p": "p.Asp149Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016878131.1",
"strand": true,
"transcript": "XM_017022642.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 807,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000556382.1",
"gene_hgnc_id": 10870,
"gene_symbol": "ST8SIA2",
"hgvs_c": "n.152G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000556382.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs532326502",
"effect": "missense_variant",
"frequency_reference_population": 0.000052039322,
"gene_hgnc_id": 10870,
"gene_symbol": "ST8SIA2",
"gnomad_exomes_ac": 77,
"gnomad_exomes_af": 0.0000526714,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 7,
"gnomad_genomes_af": 0.000045971,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.309,
"pos": 92438444,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.222,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006011.4"
}
]
}