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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: 4-88038489-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=88038489&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 88038489,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000237596.7",
"consequences": [
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Arg361Gln",
"transcript": "NM_000297.4",
"protein_id": "NP_000288.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 968,
"cds_start": 1082,
"cds_end": null,
"cds_length": 2907,
"cdna_start": 1181,
"cdna_end": null,
"cdna_length": 5089,
"mane_select": "ENST00000237596.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Arg361Gln",
"transcript": "ENST00000237596.7",
"protein_id": "ENSP00000237596.2",
"transcript_support_level": 1,
"aa_start": 361,
"aa_end": null,
"aa_length": 968,
"cds_start": 1082,
"cds_end": null,
"cds_length": 2907,
"cdna_start": 1181,
"cdna_end": null,
"cdna_length": 5089,
"mane_select": "NM_000297.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Arg361Gln",
"transcript": "NM_001440544.1",
"protein_id": "NP_001427473.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 893,
"cds_start": 1082,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 1181,
"cdna_end": null,
"cdna_length": 4864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.362G>A",
"hgvs_p": "p.Arg121Gln",
"transcript": "XM_011532029.2",
"protein_id": "XP_011530331.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 728,
"cds_start": 362,
"cds_end": null,
"cds_length": 2187,
"cdna_start": 459,
"cdna_end": null,
"cdna_length": 4367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.242G>A",
"hgvs_p": "p.Arg81Gln",
"transcript": "XM_011532030.3",
"protein_id": "XP_011530332.1",
"transcript_support_level": null,
"aa_start": 81,
"aa_end": null,
"aa_length": 688,
"cds_start": 242,
"cds_end": null,
"cds_length": 2067,
"cdna_start": 501,
"cdna_end": null,
"cdna_length": 4409,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "n.529G>A",
"hgvs_p": null,
"transcript": "ENST00000506367.1",
"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": 693,
"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": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "n.1181G>A",
"hgvs_p": null,
"transcript": "NR_156488.2",
"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": 4968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "n.*118G>A",
"hgvs_p": null,
"transcript": "ENST00000506727.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"dbsnp": "rs753359659",
"frequency_reference_population": 0.00008675198,
"hom_count_reference_population": 3,
"allele_count_reference_population": 140,
"gnomad_exomes_af": 0.0000615758,
"gnomad_genomes_af": 0.000328554,
"gnomad_exomes_ac": 90,
"gnomad_genomes_ac": 50,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04085472226142883,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.059,
"revel_prediction": "Benign",
"alphamissense_score": 0.0797,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.298,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -18,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 20,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000237596.7",
"gene_symbol": "PKD2",
"hgnc_id": 9009,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Arg361Gln"
}
],
"clinvar_disease": "Autosomal dominant polycystic kidney disease,Polycystic kidney disease 2,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3",
"phenotype_combined": "Polycystic kidney disease 2|Autosomal dominant polycystic kidney disease|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}