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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: 1-16130381-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=16130381&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 16130381,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000358432.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.2514A>G",
"hgvs_p": "p.Thr838Thr",
"transcript": "NM_004431.5",
"protein_id": "NP_004422.2",
"transcript_support_level": null,
"aa_start": 838,
"aa_end": null,
"aa_length": 976,
"cds_start": 2514,
"cds_end": null,
"cds_length": 2931,
"cdna_start": 2651,
"cdna_end": null,
"cdna_length": 3946,
"mane_select": "ENST00000358432.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.2514A>G",
"hgvs_p": "p.Thr838Thr",
"transcript": "ENST00000358432.8",
"protein_id": "ENSP00000351209.5",
"transcript_support_level": 1,
"aa_start": 838,
"aa_end": null,
"aa_length": 976,
"cds_start": 2514,
"cds_end": null,
"cds_length": 2931,
"cdna_start": 2651,
"cdna_end": null,
"cdna_length": 3946,
"mane_select": "NM_004431.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.2352A>G",
"hgvs_p": "p.Thr784Thr",
"transcript": "NM_001329090.2",
"protein_id": "NP_001316019.1",
"transcript_support_level": null,
"aa_start": 784,
"aa_end": null,
"aa_length": 922,
"cds_start": 2352,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 2583,
"cdna_end": null,
"cdna_length": 3878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.2505A>G",
"hgvs_p": "p.Thr835Thr",
"transcript": "XM_047448259.1",
"protein_id": "XP_047304215.1",
"transcript_support_level": null,
"aa_start": 835,
"aa_end": null,
"aa_length": 973,
"cds_start": 2505,
"cds_end": null,
"cds_length": 2922,
"cdna_start": 2782,
"cdna_end": null,
"cdna_length": 4077,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.2481A>G",
"hgvs_p": "p.Thr827Thr",
"transcript": "XM_047448267.1",
"protein_id": "XP_047304223.1",
"transcript_support_level": null,
"aa_start": 827,
"aa_end": null,
"aa_length": 965,
"cds_start": 2481,
"cds_end": null,
"cds_length": 2898,
"cdna_start": 4328,
"cdna_end": null,
"cdna_length": 5623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.2352A>G",
"hgvs_p": "p.Thr784Thr",
"transcript": "XM_047448272.1",
"protein_id": "XP_047304228.1",
"transcript_support_level": null,
"aa_start": 784,
"aa_end": null,
"aa_length": 922,
"cds_start": 2352,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 2486,
"cdna_end": null,
"cdna_length": 3781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"dbsnp": "rs35586310",
"frequency_reference_population": 0.0033238293,
"hom_count_reference_population": 164,
"allele_count_reference_population": 5176,
"gnomad_exomes_af": 0.00176694,
"gnomad_genomes_af": 0.0177192,
"gnomad_exomes_ac": 2483,
"gnomad_genomes_ac": 2693,
"gnomad_exomes_homalt": 72,
"gnomad_genomes_homalt": 92,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7599999904632568,
"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": -0.76,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.189,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000358432.8",
"gene_symbol": "EPHA2",
"hgnc_id": 3386,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2514A>G",
"hgvs_p": "p.Thr838Thr"
}
],
"clinvar_disease": "Cataract 6 multiple types,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "Cataract 6 multiple types|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}