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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: 17-7285729-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=7285729&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLC2A4",
"hgnc_id": 11009,
"hgvs_c": "c.1147G>A",
"hgvs_p": "p.Val383Ile",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_001042.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_score": -9,
"allele_count_reference_population": 9045,
"alphamissense_prediction": null,
"alphamissense_score": 0.0888,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.19,
"chr": "17",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Type 2 diabetes mellitus,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.009615719318389893,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 509,
"aa_ref": "V",
"aa_start": 383,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3375,
"cdna_start": 1364,
"cds_end": null,
"cds_length": 1530,
"cds_start": 1147,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001042.3",
"gene_hgnc_id": 11009,
"gene_symbol": "SLC2A4",
"hgvs_c": "c.1147G>A",
"hgvs_p": "p.Val383Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000317370.13",
"protein_coding": true,
"protein_id": "NP_001033.1",
"strand": true,
"transcript": "NM_001042.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 509,
"aa_ref": "V",
"aa_start": 383,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3375,
"cdna_start": 1364,
"cds_end": null,
"cds_length": 1530,
"cds_start": 1147,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000317370.13",
"gene_hgnc_id": 11009,
"gene_symbol": "SLC2A4",
"hgvs_c": "c.1147G>A",
"hgvs_p": "p.Val383Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001042.3",
"protein_coding": true,
"protein_id": "ENSP00000320935.8",
"strand": true,
"transcript": "ENST00000317370.13",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2995,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000572485.5",
"gene_hgnc_id": 11009,
"gene_symbol": "SLC2A4",
"hgvs_c": "n.1208G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000461086.1",
"strand": true,
"transcript": "ENST00000572485.5",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 508,
"aa_ref": "V",
"aa_start": 383,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3206,
"cdna_start": 1415,
"cds_end": null,
"cds_length": 1527,
"cds_start": 1147,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000954706.1",
"gene_hgnc_id": 11009,
"gene_symbol": "SLC2A4",
"hgvs_c": "c.1147G>A",
"hgvs_p": "p.Val383Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624765.1",
"strand": true,
"transcript": "ENST00000954706.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 507,
"aa_ref": "V",
"aa_start": 381,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2908,
"cdna_start": 1326,
"cds_end": null,
"cds_length": 1524,
"cds_start": 1141,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000859023.1",
"gene_hgnc_id": 11009,
"gene_symbol": "SLC2A4",
"hgvs_c": "c.1141G>A",
"hgvs_p": "p.Val381Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000529082.1",
"strand": true,
"transcript": "ENST00000859023.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 475,
"aa_ref": "V",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4255,
"cdna_start": 1260,
"cds_end": null,
"cds_length": 1428,
"cds_start": 1045,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000859022.1",
"gene_hgnc_id": 11009,
"gene_symbol": "SLC2A4",
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Val349Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000529081.1",
"strand": true,
"transcript": "ENST00000859022.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 461,
"aa_ref": "V",
"aa_start": 383,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1768,
"cdna_start": 1346,
"cds_end": null,
"cds_length": 1386,
"cds_start": 1147,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000571308.5",
"gene_hgnc_id": 11009,
"gene_symbol": "SLC2A4",
"hgvs_c": "c.1147G>A",
"hgvs_p": "p.Val383Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000459864.1",
"strand": true,
"transcript": "ENST00000571308.5",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 451,
"aa_ref": "V",
"aa_start": 373,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1852,
"cdna_start": 1414,
"cds_end": null,
"cds_length": 1356,
"cds_start": 1117,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000424875.2",
"gene_hgnc_id": 11009,
"gene_symbol": "SLC2A4",
"hgvs_c": "c.1117G>A",
"hgvs_p": "p.Val373Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000396887.2",
"strand": true,
"transcript": "ENST00000424875.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1813,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000570783.5",
"gene_hgnc_id": 11009,
"gene_symbol": "SLC2A4",
"hgvs_c": "n.*371G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000459056.1",
"strand": true,
"transcript": "ENST00000570783.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1813,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000570783.5",
"gene_hgnc_id": 11009,
"gene_symbol": "SLC2A4",
"hgvs_c": "n.*371G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000459056.1",
"strand": true,
"transcript": "ENST00000570783.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs121434581",
"effect": "missense_variant",
"frequency_reference_population": 0.0056034783,
"gene_hgnc_id": 11009,
"gene_symbol": "SLC2A4",
"gnomad_exomes_ac": 8430,
"gnomad_exomes_af": 0.00576656,
"gnomad_exomes_homalt": 30,
"gnomad_genomes_ac": 615,
"gnomad_genomes_af": 0.00403808,
"gnomad_genomes_homalt": 3,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 33,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Type 2 diabetes mellitus|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.253,
"pos": 7285729,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.385,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001042.3"
}
]
}