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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: 4-94334588-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=94334588&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 94334588,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_014485.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGDS",
"gene_hgnc_id": 17890,
"hgvs_c": "c.42A>G",
"hgvs_p": "p.Arg14Arg",
"transcript": "NM_014485.3",
"protein_id": "NP_055300.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 199,
"cds_start": 42,
"cds_end": null,
"cds_length": 600,
"cdna_start": 93,
"cdna_end": null,
"cdna_length": 1596,
"mane_select": "ENST00000295256.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014485.3"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGDS",
"gene_hgnc_id": 17890,
"hgvs_c": "c.42A>G",
"hgvs_p": "p.Arg14Arg",
"transcript": "ENST00000295256.10",
"protein_id": "ENSP00000295256.5",
"transcript_support_level": 1,
"aa_start": 14,
"aa_end": null,
"aa_length": 199,
"cds_start": 42,
"cds_end": null,
"cds_length": 600,
"cdna_start": 93,
"cdna_end": null,
"cdna_length": 1596,
"mane_select": "NM_014485.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295256.10"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGDS",
"gene_hgnc_id": 17890,
"hgvs_c": "c.42A>G",
"hgvs_p": "p.Arg14Arg",
"transcript": "ENST00000944232.1",
"protein_id": "ENSP00000614291.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 168,
"cds_start": 42,
"cds_end": null,
"cds_length": 507,
"cdna_start": 107,
"cdna_end": null,
"cdna_length": 1545,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944232.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGDS",
"gene_hgnc_id": 17890,
"hgvs_c": "c.42A>G",
"hgvs_p": "p.Arg14Arg",
"transcript": "XM_005262932.4",
"protein_id": "XP_005262989.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 168,
"cds_start": 42,
"cds_end": null,
"cds_length": 507,
"cdna_start": 93,
"cdna_end": null,
"cdna_length": 1503,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005262932.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGDS",
"gene_hgnc_id": 17890,
"hgvs_c": "n.133A>G",
"hgvs_p": null,
"transcript": "ENST00000506331.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 540,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000506331.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGDS",
"gene_hgnc_id": 17890,
"hgvs_c": "n.122A>G",
"hgvs_p": null,
"transcript": "ENST00000514774.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 575,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000514774.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000287552",
"gene_hgnc_id": 58855,
"hgvs_c": "n.2871-8356T>C",
"hgvs_p": null,
"transcript": "ENST00000667612.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2968,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000667612.1"
}
],
"gene_symbol": "HPGDS",
"gene_hgnc_id": 17890,
"dbsnp": "rs148378201",
"frequency_reference_population": 0.0025995793,
"hom_count_reference_population": 129,
"allele_count_reference_population": 4194,
"gnomad_exomes_af": 0.00229763,
"gnomad_genomes_af": 0.00549681,
"gnomad_exomes_ac": 3357,
"gnomad_genomes_ac": 837,
"gnomad_exomes_homalt": 104,
"gnomad_genomes_homalt": 25,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5199999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.15000000596046448,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.293,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.15,
"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": "NM_014485.3",
"gene_symbol": "HPGDS",
"hgnc_id": 17890,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.42A>G",
"hgvs_p": "p.Arg14Arg"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000667612.1",
"gene_symbol": "ENSG00000287552",
"hgnc_id": 58855,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2871-8356T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}