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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: 16-81133578-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=81133578&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PKD1L2",
"hgnc_id": 21715,
"hgvs_c": "c.5842A>T",
"hgvs_p": "p.Ile1948Phe",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000525539.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 10,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.02,
"chr": "16",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": -0.019999999552965164,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2458,
"aa_ref": "I",
"aa_start": 1948,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7379,
"cdna_start": 5842,
"cds_end": null,
"cds_length": 7379,
"cds_start": 5842,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000525539.5",
"gene_hgnc_id": 21715,
"gene_symbol": "PKD1L2",
"hgvs_c": "c.5842A>T",
"hgvs_p": "p.Ile1948Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000434417.1",
"strand": false,
"transcript": "ENST00000525539.5",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1773,
"aa_ref": "I",
"aa_start": 1263,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5669,
"cdna_start": 3898,
"cds_end": null,
"cds_length": 5324,
"cds_start": 3787,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000533478.5",
"gene_hgnc_id": 21715,
"gene_symbol": "PKD1L2",
"hgvs_c": "c.3787A>T",
"hgvs_p": "p.Ile1263Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000434644.1",
"strand": false,
"transcript": "ENST00000533478.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1608,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000530363.5",
"gene_hgnc_id": 21715,
"gene_symbol": "PKD1L2",
"hgvs_c": "n.423A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000530363.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 5818,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 25,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000299598.11",
"gene_hgnc_id": 21715,
"gene_symbol": "PKD1L2",
"hgvs_c": "n.5239A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000299598.11",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2012,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000534142.5",
"gene_hgnc_id": 21715,
"gene_symbol": "PKD1L2",
"hgvs_c": "n.231A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000534142.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 7642,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 43,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "NR_126532.3",
"gene_hgnc_id": 21715,
"gene_symbol": "PKD1L2",
"hgvs_c": "n.5857A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_126532.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs767659011",
"effect": "missense_variant",
"frequency_reference_population": 0.0000061962473,
"gene_hgnc_id": 21715,
"gene_symbol": "PKD1L2",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.00000205242,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 7,
"gnomad_genomes_af": 0.0000459951,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.499,
"pos": 81133578,
"ref": "T",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "ENST00000525539.5"
}
]
}