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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: 3-89472575-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=89472575&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 89472575,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000336596.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA3",
"gene_hgnc_id": 3387,
"hgvs_c": "c.2802T>C",
"hgvs_p": "p.Gly934Gly",
"transcript": "NM_005233.6",
"protein_id": "NP_005224.2",
"transcript_support_level": null,
"aa_start": 934,
"aa_end": null,
"aa_length": 983,
"cds_start": 2802,
"cds_end": null,
"cds_length": 2952,
"cdna_start": 2930,
"cdna_end": null,
"cdna_length": 5712,
"mane_select": "ENST00000336596.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA3",
"gene_hgnc_id": 3387,
"hgvs_c": "c.2802T>C",
"hgvs_p": "p.Gly934Gly",
"transcript": "ENST00000336596.7",
"protein_id": "ENSP00000337451.2",
"transcript_support_level": 1,
"aa_start": 934,
"aa_end": null,
"aa_length": 983,
"cds_start": 2802,
"cds_end": null,
"cds_length": 2952,
"cdna_start": 2930,
"cdna_end": null,
"cdna_length": 5712,
"mane_select": "NM_005233.6",
"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": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "EPHA3",
"gene_hgnc_id": 3387,
"hgvs_c": "c.2749+53T>C",
"hgvs_p": null,
"transcript": "ENST00000494014.1",
"protein_id": "ENSP00000419190.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 918,
"cds_start": -4,
"cds_end": null,
"cds_length": 2757,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA3",
"gene_hgnc_id": 3387,
"hgvs_c": "c.2799T>C",
"hgvs_p": "p.Gly933Gly",
"transcript": "XM_005264715.4",
"protein_id": "XP_005264772.1",
"transcript_support_level": null,
"aa_start": 933,
"aa_end": null,
"aa_length": 982,
"cds_start": 2799,
"cds_end": null,
"cds_length": 2949,
"cdna_start": 2927,
"cdna_end": null,
"cdna_length": 5709,
"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": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "EPHA3",
"gene_hgnc_id": 3387,
"hgvs_c": "c.2749+53T>C",
"hgvs_p": null,
"transcript": "NM_001410778.1",
"protein_id": "NP_001397707.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 918,
"cds_start": -4,
"cds_end": null,
"cds_length": 2757,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5615,
"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": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "EPHA3",
"gene_hgnc_id": 3387,
"hgvs_c": "c.2746+53T>C",
"hgvs_p": null,
"transcript": "XM_047447673.1",
"protein_id": "XP_047303629.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 917,
"cds_start": -4,
"cds_end": null,
"cds_length": 2754,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EPHA3",
"gene_hgnc_id": 3387,
"dbsnp": "rs1054750",
"frequency_reference_population": 0.22711475,
"hom_count_reference_population": 45489,
"allele_count_reference_population": 366342,
"gnomad_exomes_af": 0.230867,
"gnomad_genomes_af": 0.191075,
"gnomad_exomes_ac": 337281,
"gnomad_genomes_ac": 29061,
"gnomad_exomes_homalt": 42115,
"gnomad_genomes_homalt": 3374,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6200000047683716,
"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": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.254,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BA1",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000336596.7",
"gene_symbol": "EPHA3",
"hgnc_id": 3387,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2802T>C",
"hgvs_p": "p.Gly934Gly"
}
],
"clinvar_disease": "EPHA3-related disorder",
"clinvar_classification": "Benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "EPHA3-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}