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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: X-107238994-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=107238994&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 107238994,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000372453.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAAF6",
"gene_hgnc_id": 28570,
"hgvs_c": "c.502C>T",
"hgvs_p": "p.Arg168Cys",
"transcript": "NM_173494.2",
"protein_id": "NP_775765.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 214,
"cds_start": 502,
"cds_end": null,
"cds_length": 645,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 1677,
"mane_select": "ENST00000372453.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAAF6",
"gene_hgnc_id": 28570,
"hgvs_c": "c.502C>T",
"hgvs_p": "p.Arg168Cys",
"transcript": "ENST00000372453.8",
"protein_id": "ENSP00000361531.3",
"transcript_support_level": 1,
"aa_start": 168,
"aa_end": null,
"aa_length": 214,
"cds_start": 502,
"cds_end": null,
"cds_length": 645,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 1677,
"mane_select": "NM_173494.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAAF6",
"gene_hgnc_id": 28570,
"hgvs_c": "c.502C>T",
"hgvs_p": "p.Arg168Cys",
"transcript": "NM_001169154.2",
"protein_id": "NP_001162625.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 214,
"cds_start": 502,
"cds_end": null,
"cds_length": 645,
"cdna_start": 860,
"cdna_end": null,
"cdna_length": 1952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAAF6",
"gene_hgnc_id": 28570,
"hgvs_c": "c.502C>T",
"hgvs_p": "p.Arg168Cys",
"transcript": "ENST00000336387.4",
"protein_id": "ENSP00000337757.4",
"transcript_support_level": 5,
"aa_start": 168,
"aa_end": null,
"aa_length": 214,
"cds_start": 502,
"cds_end": null,
"cds_length": 645,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAAF6",
"gene_hgnc_id": 28570,
"hgvs_c": "c.502C>T",
"hgvs_p": "p.Arg168Cys",
"transcript": "ENST00000535523.6",
"protein_id": "ENSP00000441930.1",
"transcript_support_level": 5,
"aa_start": 168,
"aa_end": null,
"aa_length": 214,
"cds_start": 502,
"cds_end": null,
"cds_length": 645,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 1882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAAF6",
"gene_hgnc_id": 28570,
"hgvs_c": "c.405C>T",
"hgvs_p": "p.Phe135Phe",
"transcript": "ENST00000688816.1",
"protein_id": "ENSP00000508655.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 142,
"cds_start": 405,
"cds_end": null,
"cds_length": 429,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 1580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAAF6",
"gene_hgnc_id": 28570,
"dbsnp": "rs775335375",
"frequency_reference_population": 0.000053829826,
"hom_count_reference_population": 25,
"allele_count_reference_population": 65,
"gnomad_exomes_af": 0.0000547459,
"gnomad_genomes_af": 0.0000448282,
"gnomad_exomes_ac": 60,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.32592105865478516,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.14,
"revel_prediction": "Benign",
"alphamissense_score": 0.3513,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.048,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000372453.8",
"gene_symbol": "DNAAF6",
"hgnc_id": 28570,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.502C>T",
"hgvs_p": "p.Arg168Cys"
}
],
"clinvar_disease": " 36, X-linked, primary,Ciliary dyskinesia,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Ciliary dyskinesia, primary, 36, X-linked|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}