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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: 1-24902256-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=24902256&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 8,
"criteria": [
"BP4_Strong",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RUNX3",
"hgnc_id": 10473,
"hgvs_c": "c.1156G>A",
"hgvs_p": "p.Ala386Thr",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -8,
"transcript": "NM_001031680.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_score": -8,
"allele_count_reference_population": 980,
"alphamissense_prediction": null,
"alphamissense_score": 0.0657,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.22,
"chr": "1",
"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": 0.043292731046676636,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 415,
"aa_ref": "A",
"aa_start": 372,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4267,
"cdna_start": 1522,
"cds_end": null,
"cds_length": 1248,
"cds_start": 1114,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_004350.3",
"gene_hgnc_id": 10473,
"gene_symbol": "RUNX3",
"hgvs_c": "c.1114G>A",
"hgvs_p": "p.Ala372Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000308873.11",
"protein_coding": true,
"protein_id": "NP_004341.1",
"strand": false,
"transcript": "NM_004350.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 415,
"aa_ref": "A",
"aa_start": 372,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4267,
"cdna_start": 1522,
"cds_end": null,
"cds_length": 1248,
"cds_start": 1114,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000308873.11",
"gene_hgnc_id": 10473,
"gene_symbol": "RUNX3",
"hgvs_c": "c.1114G>A",
"hgvs_p": "p.Ala372Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004350.3",
"protein_coding": true,
"protein_id": "ENSP00000308051.6",
"strand": false,
"transcript": "ENST00000308873.11",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 429,
"aa_ref": "A",
"aa_start": 386,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4173,
"cdna_start": 1428,
"cds_end": null,
"cds_length": 1290,
"cds_start": 1156,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000338888.4",
"gene_hgnc_id": 10473,
"gene_symbol": "RUNX3",
"hgvs_c": "c.1156G>A",
"hgvs_p": "p.Ala386Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000343477.3",
"strand": false,
"transcript": "ENST00000338888.4",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 429,
"aa_ref": "A",
"aa_start": 386,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4340,
"cdna_start": 1595,
"cds_end": null,
"cds_length": 1290,
"cds_start": 1156,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001031680.2",
"gene_hgnc_id": 10473,
"gene_symbol": "RUNX3",
"hgvs_c": "c.1156G>A",
"hgvs_p": "p.Ala386Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001026850.1",
"strand": false,
"transcript": "NM_001031680.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 429,
"aa_ref": "A",
"aa_start": 386,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4173,
"cdna_start": 1428,
"cds_end": null,
"cds_length": 1290,
"cds_start": 1156,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001320672.1",
"gene_hgnc_id": 10473,
"gene_symbol": "RUNX3",
"hgvs_c": "c.1156G>A",
"hgvs_p": "p.Ala386Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001307601.1",
"strand": false,
"transcript": "NM_001320672.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 429,
"aa_ref": "A",
"aa_start": 386,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4340,
"cdna_start": 1595,
"cds_end": null,
"cds_length": 1290,
"cds_start": 1156,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000399916.5",
"gene_hgnc_id": 10473,
"gene_symbol": "RUNX3",
"hgvs_c": "c.1156G>A",
"hgvs_p": "p.Ala386Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000382800.1",
"strand": false,
"transcript": "ENST00000399916.5",
"transcript_support_level": 2
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 429,
"aa_ref": "A",
"aa_start": 386,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4028,
"cdna_start": 1283,
"cds_end": null,
"cds_length": 1290,
"cds_start": 1156,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_005246024.5",
"gene_hgnc_id": 10473,
"gene_symbol": "RUNX3",
"hgvs_c": "c.1156G>A",
"hgvs_p": "p.Ala386Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005246081.1",
"strand": false,
"transcript": "XM_005246024.5",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 429,
"aa_ref": "A",
"aa_start": 386,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4117,
"cdna_start": 1372,
"cds_end": null,
"cds_length": 1290,
"cds_start": 1156,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047433131.1",
"gene_hgnc_id": 10473,
"gene_symbol": "RUNX3",
"hgvs_c": "c.1156G>A",
"hgvs_p": "p.Ala386Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047289087.1",
"strand": false,
"transcript": "XM_047433131.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 376,
"aa_ref": "A",
"aa_start": 333,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4181,
"cdna_start": 1436,
"cds_end": null,
"cds_length": 1131,
"cds_start": 997,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011542351.2",
"gene_hgnc_id": 10473,
"gene_symbol": "RUNX3",
"hgvs_c": "c.997G>A",
"hgvs_p": "p.Ala333Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011540653.1",
"strand": false,
"transcript": "XM_011542351.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs142303780",
"effect": "missense_variant",
"frequency_reference_population": 0.0006172474,
"gene_hgnc_id": 10473,
"gene_symbol": "RUNX3",
"gnomad_exomes_ac": 923,
"gnomad_exomes_af": 0.000642991,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 57,
"gnomad_genomes_af": 0.000374468,
"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": "Benign",
"phylop100way_score": 1.51,
"pos": 24902256,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.283,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001031680.2"
}
]
}