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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: 1-25862845-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=25862845&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 25862845,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000675840.1",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR7",
"gene_hgnc_id": 23146,
"hgvs_c": "c.995T>C",
"hgvs_p": "p.Leu332Pro",
"transcript": "NM_178422.6",
"protein_id": "NP_848509.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 346,
"cds_start": 995,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 1324,
"cdna_end": null,
"cdna_length": 2685,
"mane_select": "ENST00000675840.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR7",
"gene_hgnc_id": 23146,
"hgvs_c": "c.995T>C",
"hgvs_p": "p.Leu332Pro",
"transcript": "ENST00000675840.1",
"protein_id": "ENSP00000502514.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 346,
"cds_start": 995,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 1324,
"cdna_end": null,
"cdna_length": 2685,
"mane_select": "NM_178422.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR7",
"gene_hgnc_id": 23146,
"hgvs_c": "c.995T>C",
"hgvs_p": "p.Leu332Pro",
"transcript": "ENST00000374296.4",
"protein_id": "ENSP00000363414.3",
"transcript_support_level": 1,
"aa_start": 332,
"aa_end": null,
"aa_length": 346,
"cds_start": 995,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 1662,
"cdna_end": null,
"cdna_length": 3023,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR7",
"gene_hgnc_id": 23146,
"hgvs_c": "c.995T>C",
"hgvs_p": "p.Leu332Pro",
"transcript": "XM_005245746.4",
"protein_id": "XP_005245803.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 346,
"cds_start": 995,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 1238,
"cdna_end": null,
"cdna_length": 2599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR7",
"gene_hgnc_id": 23146,
"hgvs_c": "c.995T>C",
"hgvs_p": "p.Leu332Pro",
"transcript": "XM_011540862.3",
"protein_id": "XP_011539164.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 346,
"cds_start": 995,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 1411,
"cdna_end": null,
"cdna_length": 2772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR7",
"gene_hgnc_id": 23146,
"hgvs_c": "c.995T>C",
"hgvs_p": "p.Leu332Pro",
"transcript": "XM_047447964.1",
"protein_id": "XP_047303920.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 346,
"cds_start": 995,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 5800,
"cdna_end": null,
"cdna_length": 7161,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "ENSG00000236528",
"gene_hgnc_id": null,
"hgvs_c": "n.274A>G",
"hgvs_p": null,
"transcript": "ENST00000455431.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 849,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "ENSG00000236528",
"gene_hgnc_id": null,
"hgvs_c": "n.387A>G",
"hgvs_p": null,
"transcript": "ENST00000775351.1",
"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": 1664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236528",
"gene_hgnc_id": null,
"hgvs_c": "n.296+2970A>G",
"hgvs_p": null,
"transcript": "ENST00000775349.1",
"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": 620,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236528",
"gene_hgnc_id": null,
"hgvs_c": "n.296+2970A>G",
"hgvs_p": null,
"transcript": "ENST00000775350.1",
"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": 518,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236528",
"gene_hgnc_id": null,
"hgvs_c": "n.294-1121A>G",
"hgvs_p": null,
"transcript": "ENST00000775352.1",
"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": 450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PAQR7",
"gene_hgnc_id": 23146,
"dbsnp": "rs757320225",
"frequency_reference_population": 0.00014808793,
"hom_count_reference_population": 0,
"allele_count_reference_population": 239,
"gnomad_exomes_af": 0.000155282,
"gnomad_genomes_af": 0.0000789204,
"gnomad_exomes_ac": 227,
"gnomad_genomes_ac": 12,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3642004728317261,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.204,
"revel_prediction": "Benign",
"alphamissense_score": 0.4409,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.666,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "ENST00000675840.1",
"gene_symbol": "PAQR7",
"hgnc_id": 23146,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.995T>C",
"hgvs_p": "p.Leu332Pro"
},
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "ENST00000455431.1",
"gene_symbol": "ENSG00000236528",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.274A>G",
"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
}