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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: 5-176881530-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=176881530&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 176881530,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002115.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.2399G>T",
"hgvs_p": "p.Ser800Ile",
"transcript": "NM_002115.3",
"protein_id": "NP_002106.2",
"transcript_support_level": null,
"aa_start": 800,
"aa_end": null,
"aa_length": 923,
"cds_start": 2399,
"cds_end": null,
"cds_length": 2772,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000292432.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002115.3"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.2399G>T",
"hgvs_p": "p.Ser800Ile",
"transcript": "ENST00000292432.10",
"protein_id": "ENSP00000292432.5",
"transcript_support_level": 1,
"aa_start": 800,
"aa_end": null,
"aa_length": 923,
"cds_start": 2399,
"cds_end": null,
"cds_length": 2772,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002115.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000292432.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "n.1411G>T",
"hgvs_p": null,
"transcript": "ENST00000506834.5",
"protein_id": null,
"transcript_support_level": 1,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000506834.5"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.2399G>T",
"hgvs_p": "p.Ser800Ile",
"transcript": "ENST00000874508.1",
"protein_id": "ENSP00000544567.1",
"transcript_support_level": null,
"aa_start": 800,
"aa_end": null,
"aa_length": 923,
"cds_start": 2399,
"cds_end": null,
"cds_length": 2772,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874508.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.2393G>T",
"hgvs_p": "p.Ser798Ile",
"transcript": "ENST00000970949.1",
"protein_id": "ENSP00000641008.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 921,
"cds_start": 2393,
"cds_end": null,
"cds_length": 2766,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970949.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.2375G>T",
"hgvs_p": "p.Ser792Ile",
"transcript": "ENST00000970953.1",
"protein_id": "ENSP00000641012.1",
"transcript_support_level": null,
"aa_start": 792,
"aa_end": null,
"aa_length": 915,
"cds_start": 2375,
"cds_end": null,
"cds_length": 2748,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970953.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.2294G>T",
"hgvs_p": "p.Ser765Ile",
"transcript": "ENST00000970952.1",
"protein_id": "ENSP00000641011.1",
"transcript_support_level": null,
"aa_start": 765,
"aa_end": null,
"aa_length": 888,
"cds_start": 2294,
"cds_end": null,
"cds_length": 2667,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970952.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.2279G>T",
"hgvs_p": "p.Ser760Ile",
"transcript": "ENST00000970951.1",
"protein_id": "ENSP00000641010.1",
"transcript_support_level": null,
"aa_start": 760,
"aa_end": null,
"aa_length": 883,
"cds_start": 2279,
"cds_end": null,
"cds_length": 2652,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970951.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.2165G>T",
"hgvs_p": "p.Ser722Ile",
"transcript": "ENST00000970948.1",
"protein_id": "ENSP00000641007.1",
"transcript_support_level": null,
"aa_start": 722,
"aa_end": null,
"aa_length": 845,
"cds_start": 2165,
"cds_end": null,
"cds_length": 2538,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970948.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.2165G>T",
"hgvs_p": "p.Ser722Ile",
"transcript": "ENST00000970950.1",
"protein_id": "ENSP00000641009.1",
"transcript_support_level": null,
"aa_start": 722,
"aa_end": null,
"aa_length": 845,
"cds_start": 2165,
"cds_end": null,
"cds_length": 2538,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970950.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.1631G>T",
"hgvs_p": "p.Ser544Ile",
"transcript": "ENST00000970954.1",
"protein_id": "ENSP00000641013.1",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 667,
"cds_start": 1631,
"cds_end": null,
"cds_length": 2004,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970954.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.2302G>T",
"hgvs_p": "p.Ala768Ser",
"transcript": "XM_047417134.1",
"protein_id": "XP_047273090.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 777,
"cds_start": 2302,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417134.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "c.2394-1G>T",
"hgvs_p": null,
"transcript": "ENST00000970955.1",
"protein_id": "ENSP00000641014.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 921,
"cds_start": null,
"cds_end": null,
"cds_length": 2766,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970955.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"hgvs_c": "n.187G>T",
"hgvs_p": null,
"transcript": "ENST00000514666.1",
"protein_id": null,
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000514666.1"
}
],
"gene_symbol": "HK3",
"gene_hgnc_id": 4925,
"dbsnp": "rs540302092",
"frequency_reference_population": 0.0000013795349,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000137953,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.38485339283943176,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.15000000596046448,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.421,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2446,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.862,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002115.3",
"gene_symbol": "HK3",
"hgnc_id": 4925,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2399G>T",
"hgvs_p": "p.Ser800Ile"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}