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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: 1-26900369-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=26900369&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 26900369,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_022078.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPATCH3",
"gene_hgnc_id": 25720,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Arg25His",
"transcript": "NM_022078.3",
"protein_id": "NP_071361.2",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 525,
"cds_start": 74,
"cds_end": null,
"cds_length": 1578,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000361720.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022078.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPATCH3",
"gene_hgnc_id": 25720,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Arg25His",
"transcript": "ENST00000361720.10",
"protein_id": "ENSP00000354645.5",
"transcript_support_level": 1,
"aa_start": 25,
"aa_end": null,
"aa_length": 525,
"cds_start": 74,
"cds_end": null,
"cds_length": 1578,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_022078.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361720.10"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPATCH3",
"gene_hgnc_id": 25720,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Arg25His",
"transcript": "ENST00000945224.1",
"protein_id": "ENSP00000615283.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 516,
"cds_start": 74,
"cds_end": null,
"cds_length": 1551,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945224.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPATCH3",
"gene_hgnc_id": 25720,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Arg25His",
"transcript": "XM_047427518.1",
"protein_id": "XP_047283474.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 320,
"cds_start": 74,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047427518.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDC",
"gene_hgnc_id": 8045,
"hgvs_c": "c.-132C>T",
"hgvs_p": null,
"transcript": "ENST00000435827.6",
"protein_id": "ENSP00000404020.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 185,
"cds_start": null,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000435827.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDC",
"gene_hgnc_id": 8045,
"hgvs_c": "c.-812C>T",
"hgvs_p": null,
"transcript": "XM_047439143.1",
"protein_id": "XP_047295099.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 335,
"cds_start": null,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439143.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDC",
"gene_hgnc_id": 8045,
"hgvs_c": "c.-727C>T",
"hgvs_p": null,
"transcript": "XM_047439206.1",
"protein_id": "XP_047295162.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 335,
"cds_start": null,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439206.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDC",
"gene_hgnc_id": 8045,
"hgvs_c": "c.-453C>T",
"hgvs_p": null,
"transcript": "XM_024452486.2",
"protein_id": "XP_024308254.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 335,
"cds_start": null,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024452486.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDC",
"gene_hgnc_id": 8045,
"hgvs_c": "c.-368C>T",
"hgvs_p": null,
"transcript": "XM_047439200.1",
"protein_id": "XP_047295156.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 335,
"cds_start": null,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439200.1"
}
],
"gene_symbol": "GPATCH3",
"gene_hgnc_id": 25720,
"dbsnp": "rs149540976",
"frequency_reference_population": 0.000013631576,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000095776,
"gnomad_genomes_af": 0.0000525776,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.26174578070640564,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.141,
"revel_prediction": "Benign",
"alphamissense_score": 0.1207,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.16,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.528,
"phylop100way_prediction": "Uncertain_significance",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_022078.3",
"gene_symbol": "GPATCH3",
"hgnc_id": 25720,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Arg25His"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000435827.6",
"gene_symbol": "NUDC",
"hgnc_id": 8045,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-132C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}