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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: 12-80444765-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=80444765&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 80444765,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001145026.2",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Gly27Arg",
"transcript": "NM_001145026.2",
"protein_id": "NP_001138498.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 2299,
"cds_start": 79,
"cds_end": null,
"cds_length": 6900,
"cdna_start": 190,
"cdna_end": null,
"cdna_length": 8261,
"mane_select": "ENST00000644991.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145026.2"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Gly27Arg",
"transcript": "ENST00000644991.3",
"protein_id": "ENSP00000495607.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 2299,
"cds_start": 79,
"cds_end": null,
"cds_length": 6900,
"cdna_start": 190,
"cdna_end": null,
"cdna_length": 8261,
"mane_select": "NM_001145026.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644991.3"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.205G>C",
"hgvs_p": "p.Gly69Arg",
"transcript": "ENST00000616559.4",
"protein_id": "ENSP00000483259.1",
"transcript_support_level": 5,
"aa_start": 69,
"aa_end": null,
"aa_length": 2332,
"cds_start": 205,
"cds_end": null,
"cds_length": 6999,
"cdna_start": 205,
"cdna_end": null,
"cdna_length": 8165,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000616559.4"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.943G>C",
"hgvs_p": "p.Gly315Arg",
"transcript": "ENST00000547376.5",
"protein_id": "ENSP00000448844.1",
"transcript_support_level": 5,
"aa_start": 315,
"aa_end": null,
"aa_length": 352,
"cds_start": 943,
"cds_end": null,
"cds_length": 1061,
"cdna_start": 1582,
"cdna_end": null,
"cdna_length": 1700,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000547376.5"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.685G>C",
"hgvs_p": "p.Gly229Arg",
"transcript": "ENST00000551042.5",
"protein_id": "ENSP00000447522.1",
"transcript_support_level": 5,
"aa_start": 229,
"aa_end": null,
"aa_length": 331,
"cds_start": 685,
"cds_end": null,
"cds_length": 996,
"cdna_start": 2025,
"cdna_end": null,
"cdna_length": 2336,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000551042.5"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.733G>C",
"hgvs_p": "p.Gly245Arg",
"transcript": "ENST00000551573.5",
"protein_id": "ENSP00000449133.1",
"transcript_support_level": 3,
"aa_start": 245,
"aa_end": null,
"aa_length": 282,
"cds_start": 733,
"cds_end": null,
"cds_length": 851,
"cdna_start": 979,
"cdna_end": null,
"cdna_length": 1097,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000551573.5"
}
],
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"dbsnp": "rs1397975118",
"frequency_reference_population": 0.0000072073008,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.0000072073,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8725370168685913,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.14000000059604645,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.425,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.298,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.497,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.14,
"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": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001145026.2",
"gene_symbol": "PTPRQ",
"hgnc_id": 9679,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown,AD,SD",
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Gly27Arg"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}