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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: 12-80670476-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=80670476&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 80670476,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000644991.3",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.6586A>G",
"hgvs_p": "p.Met2196Val",
"transcript": "NM_001145026.2",
"protein_id": "NP_001138498.1",
"transcript_support_level": null,
"aa_start": 2196,
"aa_end": null,
"aa_length": 2299,
"cds_start": 6586,
"cds_end": null,
"cds_length": 6900,
"cdna_start": 6697,
"cdna_end": null,
"cdna_length": 8261,
"mane_select": "ENST00000644991.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.6586A>G",
"hgvs_p": "p.Met2196Val",
"transcript": "ENST00000644991.3",
"protein_id": "ENSP00000495607.1",
"transcript_support_level": null,
"aa_start": 2196,
"aa_end": null,
"aa_length": 2299,
"cds_start": 6586,
"cds_end": null,
"cds_length": 6900,
"cdna_start": 6697,
"cdna_end": null,
"cdna_length": 8261,
"mane_select": "NM_001145026.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.6685A>G",
"hgvs_p": "p.Met2229Val",
"transcript": "ENST00000616559.4",
"protein_id": "ENSP00000483259.1",
"transcript_support_level": 5,
"aa_start": 2229,
"aa_end": null,
"aa_length": 2332,
"cds_start": 6685,
"cds_end": null,
"cds_length": 6999,
"cdna_start": 6685,
"cdna_end": null,
"cdna_length": 8165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000304204",
"gene_hgnc_id": null,
"hgvs_c": "n.100+36633T>C",
"hgvs_p": null,
"transcript": "ENST00000801015.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 303,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000304204",
"gene_hgnc_id": null,
"hgvs_c": "n.101-18125T>C",
"hgvs_p": null,
"transcript": "ENST00000801016.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC105369867",
"gene_hgnc_id": null,
"hgvs_c": "n.130+36633T>C",
"hgvs_p": null,
"transcript": "XR_007063388.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"dbsnp": "rs200166814",
"frequency_reference_population": 0.0020154107,
"hom_count_reference_population": 5,
"allele_count_reference_population": 3122,
"gnomad_exomes_af": 0.0020882,
"gnomad_genomes_af": 0.00134718,
"gnomad_exomes_ac": 2917,
"gnomad_genomes_ac": 205,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.028424710035324097,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.247,
"revel_prediction": "Benign",
"alphamissense_score": 0.0827,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.849,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1_Supporting",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000644991.3",
"gene_symbol": "PTPRQ",
"hgnc_id": 9679,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,SD,AD,Unknown",
"hgvs_c": "c.6586A>G",
"hgvs_p": "p.Met2196Val"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000801015.1",
"gene_symbol": "ENSG00000304204",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.100+36633T>C",
"hgvs_p": null
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "XR_007063388.1",
"gene_symbol": "LOC105369867",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.130+36633T>C",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal dominant 73, autosomal recessive,Autosomal recessive nonsyndromic hearing loss 84A,Hearing loss,PTPRQ-related disorder,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "Hearing loss, autosomal dominant 73;Autosomal recessive nonsyndromic hearing loss 84A|not provided|Hearing loss, autosomal recessive|PTPRQ-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}