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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: 5-176881762-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=176881762&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PP3_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "HK3",
"hgnc_id": 4925,
"hgvs_c": "c.2323C>T",
"hgvs_p": "p.Arg775Trp",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_002115.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_score": -2,
"allele_count_reference_population": 127,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1229,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.05,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8689931631088257,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 923,
"aa_ref": "R",
"aa_start": 775,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3082,
"cdna_start": 2429,
"cds_end": null,
"cds_length": 2772,
"cds_start": 2323,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_002115.3",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.2323C>T",
"hgvs_p": "p.Arg775Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000292432.10",
"protein_coding": true,
"protein_id": "NP_002106.2",
"strand": false,
"transcript": "NM_002115.3",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 923,
"aa_ref": "R",
"aa_start": 775,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3082,
"cdna_start": 2429,
"cds_end": null,
"cds_length": 2772,
"cds_start": 2323,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000292432.10",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.2323C>T",
"hgvs_p": "p.Arg775Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002115.3",
"protein_coding": true,
"protein_id": "ENSP00000292432.5",
"strand": false,
"transcript": "ENST00000292432.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1988,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000506834.5",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "n.1335C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000506834.5",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 923,
"aa_ref": "R",
"aa_start": 775,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3019,
"cdna_start": 2374,
"cds_end": null,
"cds_length": 2772,
"cds_start": 2323,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000874508.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.2323C>T",
"hgvs_p": "p.Arg775Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544567.1",
"strand": false,
"transcript": "ENST00000874508.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 921,
"aa_ref": "R",
"aa_start": 773,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3079,
"cdna_start": 2423,
"cds_end": null,
"cds_length": 2766,
"cds_start": 2317,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000970949.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.2317C>T",
"hgvs_p": "p.Arg773Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641008.1",
"strand": false,
"transcript": "ENST00000970949.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 921,
"aa_ref": "R",
"aa_start": 775,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3045,
"cdna_start": 2423,
"cds_end": null,
"cds_length": 2766,
"cds_start": 2323,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000970955.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.2323C>T",
"hgvs_p": "p.Arg775Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641014.1",
"strand": false,
"transcript": "ENST00000970955.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 915,
"aa_ref": "R",
"aa_start": 767,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3051,
"cdna_start": 2399,
"cds_end": null,
"cds_length": 2748,
"cds_start": 2299,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000970953.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.2299C>T",
"hgvs_p": "p.Arg767Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641012.1",
"strand": false,
"transcript": "ENST00000970953.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 888,
"aa_ref": "R",
"aa_start": 740,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2976,
"cdna_start": 2324,
"cds_end": null,
"cds_length": 2667,
"cds_start": 2218,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000970952.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.2218C>T",
"hgvs_p": "p.Arg740Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641011.1",
"strand": false,
"transcript": "ENST00000970952.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 883,
"aa_ref": "R",
"aa_start": 735,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2961,
"cdna_start": 2309,
"cds_end": null,
"cds_length": 2652,
"cds_start": 2203,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000970951.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.2203C>T",
"hgvs_p": "p.Arg735Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641010.1",
"strand": false,
"transcript": "ENST00000970951.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 845,
"aa_ref": "R",
"aa_start": 697,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2897,
"cdna_start": 2195,
"cds_end": null,
"cds_length": 2538,
"cds_start": 2089,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000970948.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.2089C>T",
"hgvs_p": "p.Arg697Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641007.1",
"strand": false,
"transcript": "ENST00000970948.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 845,
"aa_ref": "R",
"aa_start": 697,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2908,
"cdna_start": 2255,
"cds_end": null,
"cds_length": 2538,
"cds_start": 2089,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000970950.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.2089C>T",
"hgvs_p": "p.Arg697Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641009.1",
"strand": false,
"transcript": "ENST00000970950.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 667,
"aa_ref": "R",
"aa_start": 519,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2295,
"cdna_start": 1650,
"cds_end": null,
"cds_length": 2004,
"cds_start": 1555,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000970954.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.1555C>T",
"hgvs_p": "p.Arg519Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641013.1",
"strand": false,
"transcript": "ENST00000970954.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 777,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2531,
"cdna_start": null,
"cds_end": null,
"cds_length": 2334,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047417134.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.2238-12C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047273090.1",
"strand": false,
"transcript": "XM_047417134.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 415,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000514666.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "n.111C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000514666.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 130,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 395,
"cdna_start": null,
"cds_end": null,
"cds_length": 395,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000514058.1",
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"hgvs_c": "c.*194C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424632.1",
"strand": true,
"transcript": "ENST00000514058.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs145588665",
"effect": "missense_variant",
"frequency_reference_population": 0.00007867753,
"gene_hgnc_id": 4925,
"gene_symbol": "HK3",
"gnomad_exomes_ac": 115,
"gnomad_exomes_af": 0.0000786678,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 12,
"gnomad_genomes_af": 0.0000787712,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.199,
"pos": 176881762,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.741,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07999999821186066,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.08,
"transcript": "NM_002115.3"
}
]
}