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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: 1-16132282-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=16132282&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 16132282,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000358432.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.2116-9C>T",
"hgvs_p": null,
"transcript": "NM_004431.5",
"protein_id": "NP_004422.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 976,
"cds_start": -4,
"cds_end": null,
"cds_length": 2931,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3946,
"mane_select": "ENST00000358432.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.2116-9C>T",
"hgvs_p": null,
"transcript": "ENST00000358432.8",
"protein_id": "ENSP00000351209.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 976,
"cds_start": -4,
"cds_end": null,
"cds_length": 2931,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3946,
"mane_select": "NM_004431.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.1954-9C>T",
"hgvs_p": null,
"transcript": "NM_001329090.2",
"protein_id": "NP_001316019.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 922,
"cds_start": -4,
"cds_end": null,
"cds_length": 2769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.2107-9C>T",
"hgvs_p": null,
"transcript": "XM_047448259.1",
"protein_id": "XP_047304215.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 973,
"cds_start": -4,
"cds_end": null,
"cds_length": 2922,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4077,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.2083-9C>T",
"hgvs_p": null,
"transcript": "XM_047448267.1",
"protein_id": "XP_047304223.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 965,
"cds_start": -4,
"cds_end": null,
"cds_length": 2898,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"hgvs_c": "c.1954-9C>T",
"hgvs_p": null,
"transcript": "XM_047448272.1",
"protein_id": "XP_047304228.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 922,
"cds_start": -4,
"cds_end": null,
"cds_length": 2769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EPHA2",
"gene_hgnc_id": 3386,
"dbsnp": "rs753038083",
"frequency_reference_population": 0.00002292552,
"hom_count_reference_population": 0,
"allele_count_reference_population": 37,
"gnomad_exomes_af": 0.0000239446,
"gnomad_genomes_af": 0.0000131396,
"gnomad_exomes_ac": 35,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7900000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.1120000034570694,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.402,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000482274634760018,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000358432.8",
"gene_symbol": "EPHA2",
"hgnc_id": 3386,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2116-9C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Cataract 6 multiple types",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "Cataract 6 multiple types",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}