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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: 2-162373537-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=162373537&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 162373537,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_033272.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"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": "KCNH7",
"gene_hgnc_id": 18863,
"hgvs_c": "c.3257A>G",
"hgvs_p": "p.Gln1086Arg",
"transcript": "NM_033272.4",
"protein_id": "NP_150375.2",
"transcript_support_level": null,
"aa_start": 1086,
"aa_end": null,
"aa_length": 1196,
"cds_start": 3257,
"cds_end": null,
"cds_length": 3591,
"cdna_start": 3506,
"cdna_end": null,
"cdna_length": 4262,
"mane_select": "ENST00000332142.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"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": "KCNH7",
"gene_hgnc_id": 18863,
"hgvs_c": "c.3257A>G",
"hgvs_p": "p.Gln1086Arg",
"transcript": "ENST00000332142.10",
"protein_id": "ENSP00000331727.5",
"transcript_support_level": 1,
"aa_start": 1086,
"aa_end": null,
"aa_length": 1196,
"cds_start": 3257,
"cds_end": null,
"cds_length": 3591,
"cdna_start": 3506,
"cdna_end": null,
"cdna_length": 4262,
"mane_select": "NM_033272.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH7",
"gene_hgnc_id": 18863,
"hgvs_c": "c.3281A>G",
"hgvs_p": "p.Gln1094Arg",
"transcript": "XM_011512109.4",
"protein_id": "XP_011510411.1",
"transcript_support_level": null,
"aa_start": 1094,
"aa_end": null,
"aa_length": 1204,
"cds_start": 3281,
"cds_end": null,
"cds_length": 3615,
"cdna_start": 3530,
"cdna_end": null,
"cdna_length": 4286,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH7",
"gene_hgnc_id": 18863,
"hgvs_c": "c.3272A>G",
"hgvs_p": "p.Gln1091Arg",
"transcript": "XM_017005218.3",
"protein_id": "XP_016860707.1",
"transcript_support_level": null,
"aa_start": 1091,
"aa_end": null,
"aa_length": 1201,
"cds_start": 3272,
"cds_end": null,
"cds_length": 3606,
"cdna_start": 3521,
"cdna_end": null,
"cdna_length": 4277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"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": "KCNH7",
"gene_hgnc_id": 18863,
"hgvs_c": "c.3248A>G",
"hgvs_p": "p.Gln1083Arg",
"transcript": "XM_017005219.3",
"protein_id": "XP_016860708.1",
"transcript_support_level": null,
"aa_start": 1083,
"aa_end": null,
"aa_length": 1193,
"cds_start": 3248,
"cds_end": null,
"cds_length": 3582,
"cdna_start": 3497,
"cdna_end": null,
"cdna_length": 4253,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH7",
"gene_hgnc_id": 18863,
"hgvs_c": "c.3236A>G",
"hgvs_p": "p.Gln1079Arg",
"transcript": "XM_017005220.3",
"protein_id": "XP_016860709.1",
"transcript_support_level": null,
"aa_start": 1079,
"aa_end": null,
"aa_length": 1189,
"cds_start": 3236,
"cds_end": null,
"cds_length": 3570,
"cdna_start": 3485,
"cdna_end": null,
"cdna_length": 4241,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCA",
"gene_hgnc_id": 15990,
"hgvs_c": "c.*2157T>C",
"hgvs_p": null,
"transcript": "XM_005246446.4",
"protein_id": "XP_005246503.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 233,
"cds_start": -4,
"cds_end": null,
"cds_length": 702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KCNH7",
"gene_hgnc_id": 18863,
"dbsnp": "rs147827058",
"frequency_reference_population": 0.00015473994,
"hom_count_reference_population": 0,
"allele_count_reference_population": 246,
"gnomad_exomes_af": 0.000164858,
"gnomad_genomes_af": 0.0000591483,
"gnomad_exomes_ac": 237,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.042070865631103516,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.175,
"revel_prediction": "Benign",
"alphamissense_score": 0.0575,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.724,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_033272.4",
"gene_symbol": "KCNH7",
"hgnc_id": 18863,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3257A>G",
"hgvs_p": "p.Gln1086Arg"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "XM_005246446.4",
"gene_symbol": "GCA",
"hgnc_id": 15990,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*2157T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}