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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: 8-144080552-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=144080552&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 144080552,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_019037.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC4",
"gene_hgnc_id": 18189,
"hgvs_c": "c.689G>A",
"hgvs_p": "p.Arg230Gln",
"transcript": "NM_019037.3",
"protein_id": "NP_061910.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 245,
"cds_start": 689,
"cds_end": null,
"cds_length": 738,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000316052.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019037.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC4",
"gene_hgnc_id": 18189,
"hgvs_c": "c.689G>A",
"hgvs_p": "p.Arg230Gln",
"transcript": "ENST00000316052.6",
"protein_id": "ENSP00000315476.4",
"transcript_support_level": 1,
"aa_start": 230,
"aa_end": null,
"aa_length": 245,
"cds_start": 689,
"cds_end": null,
"cds_length": 738,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_019037.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000316052.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000290230",
"gene_hgnc_id": null,
"hgvs_c": "n.689G>A",
"hgvs_p": null,
"transcript": "ENST00000703646.1",
"protein_id": "ENSP00000515414.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000703646.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC4",
"gene_hgnc_id": 18189,
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280Gln",
"transcript": "ENST00000917256.1",
"protein_id": "ENSP00000587315.1",
"transcript_support_level": null,
"aa_start": 280,
"aa_end": null,
"aa_length": 295,
"cds_start": 839,
"cds_end": null,
"cds_length": 888,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917256.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC4",
"gene_hgnc_id": 18189,
"hgvs_c": "c.788G>A",
"hgvs_p": "p.Arg263Gln",
"transcript": "ENST00000917254.1",
"protein_id": "ENSP00000587313.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 278,
"cds_start": 788,
"cds_end": null,
"cds_length": 837,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917254.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC4",
"gene_hgnc_id": 18189,
"hgvs_c": "c.758G>A",
"hgvs_p": "p.Arg253Gln",
"transcript": "ENST00000527954.1",
"protein_id": "ENSP00000436539.1",
"transcript_support_level": 2,
"aa_start": 253,
"aa_end": null,
"aa_length": 260,
"cds_start": 758,
"cds_end": null,
"cds_length": 785,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000527954.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC4",
"gene_hgnc_id": 18189,
"hgvs_c": "c.683G>A",
"hgvs_p": "p.Arg228Gln",
"transcript": "ENST00000917255.1",
"protein_id": "ENSP00000587314.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 243,
"cds_start": 683,
"cds_end": null,
"cds_length": 732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917255.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC4",
"gene_hgnc_id": 18189,
"hgvs_c": "c.680G>A",
"hgvs_p": "p.Arg227Gln",
"transcript": "ENST00000905027.1",
"protein_id": "ENSP00000575086.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 242,
"cds_start": 680,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905027.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC4",
"gene_hgnc_id": 18189,
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132Gln",
"transcript": "XM_011517134.4",
"protein_id": "XP_011515436.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 147,
"cds_start": 395,
"cds_end": null,
"cds_length": 444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011517134.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000290230",
"gene_hgnc_id": null,
"hgvs_c": "n.776G>A",
"hgvs_p": null,
"transcript": "ENST00000703645.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000703645.1"
},
{
"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": "LOC124902038",
"gene_hgnc_id": null,
"hgvs_c": "n.1277C>T",
"hgvs_p": null,
"transcript": "XR_007061141.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007061141.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC4",
"gene_hgnc_id": 18189,
"hgvs_c": "c.*90G>A",
"hgvs_p": null,
"transcript": "ENST00000525936.1",
"protein_id": "ENSP00000432661.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 156,
"cds_start": null,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000525936.1"
}
],
"gene_symbol": "EXOSC4",
"gene_hgnc_id": 18189,
"dbsnp": "rs1217506792",
"frequency_reference_population": 0.000005523115,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000552311,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04062068462371826,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.059,
"revel_prediction": "Benign",
"alphamissense_score": 0.0701,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.609,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_019037.3",
"gene_symbol": "EXOSC4",
"hgnc_id": 18189,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.689G>A",
"hgvs_p": "p.Arg230Gln"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000703646.1",
"gene_symbol": "ENSG00000290230",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.689G>A",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "XR_007061141.1",
"gene_symbol": "LOC124902038",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1277C>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
}