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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: 16-81137521-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=81137521&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 81137521,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000525539.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L2",
"gene_hgnc_id": 21715,
"hgvs_c": "c.5635G>A",
"hgvs_p": "p.Ala1879Thr",
"transcript": "ENST00000525539.5",
"protein_id": "ENSP00000434417.1",
"transcript_support_level": 1,
"aa_start": 1879,
"aa_end": null,
"aa_length": 2458,
"cds_start": 5635,
"cds_end": null,
"cds_length": 7379,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000525539.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L2",
"gene_hgnc_id": 21715,
"hgvs_c": "c.3580G>A",
"hgvs_p": "p.Ala1194Thr",
"transcript": "ENST00000533478.5",
"protein_id": "ENSP00000434644.1",
"transcript_support_level": 1,
"aa_start": 1194,
"aa_end": null,
"aa_length": 1773,
"cds_start": 3580,
"cds_end": null,
"cds_length": 5324,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000533478.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L2",
"gene_hgnc_id": 21715,
"hgvs_c": "n.216G>A",
"hgvs_p": null,
"transcript": "ENST00000530363.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000530363.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L2",
"gene_hgnc_id": 21715,
"hgvs_c": "n.5032G>A",
"hgvs_p": null,
"transcript": "ENST00000299598.11",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000299598.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L2",
"gene_hgnc_id": 21715,
"hgvs_c": "n.5650G>A",
"hgvs_p": null,
"transcript": "NR_126532.3",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_126532.3"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286759",
"gene_hgnc_id": null,
"hgvs_c": "n.117+795C>T",
"hgvs_p": null,
"transcript": "ENST00000662219.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000662219.2"
},
{
"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": "ENSG00000286759",
"gene_hgnc_id": null,
"hgvs_c": "n.78+834C>T",
"hgvs_p": null,
"transcript": "ENST00000816530.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000816530.1"
}
],
"gene_symbol": "PKD1L2",
"gene_hgnc_id": 21715,
"dbsnp": "rs371765077",
"frequency_reference_population": 0.000021277581,
"hom_count_reference_population": 0,
"allele_count_reference_population": 34,
"gnomad_exomes_af": 0.0000214419,
"gnomad_genomes_af": 0.0000197163,
"gnomad_exomes_ac": 31,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3499999940395355,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.18000000715255737,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.15,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.18,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000525539.5",
"gene_symbol": "PKD1L2",
"hgnc_id": 21715,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.5635G>A",
"hgvs_p": "p.Ala1879Thr"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000662219.2",
"gene_symbol": "ENSG00000286759",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.117+795C>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}