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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: X-153803772-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153803772&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153803772,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000393758.7",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1909G>T",
"hgvs_p": "p.Asp637Tyr",
"transcript": "NM_001303512.2",
"protein_id": "NP_001290441.1",
"transcript_support_level": null,
"aa_start": 637,
"aa_end": null,
"aa_length": 775,
"cds_start": 1909,
"cds_end": null,
"cds_length": 2328,
"cdna_start": 2155,
"cdna_end": null,
"cdna_length": 3761,
"mane_select": "ENST00000393758.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1909G>T",
"hgvs_p": "p.Asp637Tyr",
"transcript": "ENST00000393758.7",
"protein_id": "ENSP00000377355.3",
"transcript_support_level": 1,
"aa_start": 637,
"aa_end": null,
"aa_length": 775,
"cds_start": 1909,
"cds_end": null,
"cds_length": 2328,
"cdna_start": 2155,
"cdna_end": null,
"cdna_length": 3761,
"mane_select": "NM_001303512.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1891G>T",
"hgvs_p": "p.Asp631Tyr",
"transcript": "ENST00000164640.8",
"protein_id": "ENSP00000164640.4",
"transcript_support_level": 1,
"aa_start": 631,
"aa_end": null,
"aa_length": 769,
"cds_start": 1891,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 2083,
"cdna_end": null,
"cdna_length": 3689,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1564G>T",
"hgvs_p": "p.Asp522Tyr",
"transcript": "ENST00000544474.5",
"protein_id": "ENSP00000442033.1",
"transcript_support_level": 1,
"aa_start": 522,
"aa_end": null,
"aa_length": 660,
"cds_start": 1564,
"cds_end": null,
"cds_length": 1983,
"cdna_start": 1814,
"cdna_end": null,
"cdna_length": 3418,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1891G>T",
"hgvs_p": "p.Asp631Tyr",
"transcript": "NM_032512.5",
"protein_id": "NP_115901.2",
"transcript_support_level": null,
"aa_start": 631,
"aa_end": null,
"aa_length": 769,
"cds_start": 1891,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 2137,
"cdna_end": null,
"cdna_length": 3743,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1666G>T",
"hgvs_p": "p.Asp556Tyr",
"transcript": "NM_001303515.2",
"protein_id": "NP_001290444.1",
"transcript_support_level": null,
"aa_start": 556,
"aa_end": null,
"aa_length": 694,
"cds_start": 1666,
"cds_end": null,
"cds_length": 2085,
"cdna_start": 2076,
"cdna_end": null,
"cdna_length": 3682,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1648G>T",
"hgvs_p": "p.Asp550Tyr",
"transcript": "NM_001303516.2",
"protein_id": "NP_001290445.1",
"transcript_support_level": null,
"aa_start": 550,
"aa_end": null,
"aa_length": 688,
"cds_start": 1648,
"cds_end": null,
"cds_length": 2067,
"cdna_start": 2058,
"cdna_end": null,
"cdna_length": 3664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1603G>T",
"hgvs_p": "p.Asp535Tyr",
"transcript": "NM_001303513.3",
"protein_id": "NP_001290442.1",
"transcript_support_level": null,
"aa_start": 535,
"aa_end": null,
"aa_length": 673,
"cds_start": 1603,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 2398,
"cdna_end": null,
"cdna_length": 4004,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1564G>T",
"hgvs_p": "p.Asp522Tyr",
"transcript": "NM_001303514.2",
"protein_id": "NP_001290443.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 660,
"cds_start": 1564,
"cds_end": null,
"cds_length": 1983,
"cdna_start": 1810,
"cdna_end": null,
"cdna_length": 3416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8714672327041626,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.67,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9982,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.25,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.097,
"phylop100way_prediction": "Uncertain_significance",
"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": 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": "ENST00000393758.7",
"gene_symbol": "PDZD4",
"hgnc_id": 21167,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1909G>T",
"hgvs_p": "p.Asp637Tyr"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}