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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: 4-88043458-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=88043458&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 88043458,
"ref": "G",
"alt": "A",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_000297.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1319+1G>A",
"hgvs_p": null,
"transcript": "NM_000297.4",
"protein_id": "NP_000288.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 968,
"cds_start": null,
"cds_end": null,
"cds_length": 2907,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000237596.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000297.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1319+1G>A",
"hgvs_p": null,
"transcript": "ENST00000237596.7",
"protein_id": "ENSP00000237596.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 968,
"cds_start": null,
"cds_end": null,
"cds_length": 2907,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000297.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000237596.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1319+1G>A",
"hgvs_p": null,
"transcript": "ENST00000927447.1",
"protein_id": "ENSP00000597506.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 967,
"cds_start": null,
"cds_end": null,
"cds_length": 2904,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927447.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1319+1G>A",
"hgvs_p": null,
"transcript": "ENST00000927448.1",
"protein_id": "ENSP00000597507.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 935,
"cds_start": null,
"cds_end": null,
"cds_length": 2808,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927448.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1205+1G>A",
"hgvs_p": null,
"transcript": "ENST00000956200.1",
"protein_id": "ENSP00000626259.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 929,
"cds_start": null,
"cds_end": null,
"cds_length": 2790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956200.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1095-3184G>A",
"hgvs_p": null,
"transcript": "NM_001440544.1",
"protein_id": "NP_001427473.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 893,
"cds_start": null,
"cds_end": null,
"cds_length": 2682,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440544.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1319+1G>A",
"hgvs_p": null,
"transcript": "ENST00000956199.1",
"protein_id": "ENSP00000626258.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 775,
"cds_start": null,
"cds_end": null,
"cds_length": 2328,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956199.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.-199+1G>A",
"hgvs_p": null,
"transcript": "ENST00000508588.5",
"protein_id": "ENSP00000427131.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 386,
"cds_start": null,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000508588.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.599+1G>A",
"hgvs_p": null,
"transcript": "XM_011532029.2",
"protein_id": "XP_011530331.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 728,
"cds_start": null,
"cds_end": null,
"cds_length": 2187,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532029.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.479+1G>A",
"hgvs_p": null,
"transcript": "XM_011532030.3",
"protein_id": "XP_011530332.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 688,
"cds_start": null,
"cds_end": null,
"cds_length": 2067,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532030.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "n.1418+1G>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": 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_156488.2"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "n.*74G>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": 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": "ENST00000506367.1"
}
],
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"dbsnp": "rs1131692280",
"frequency_reference_population": 0.0000025131121,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000138941,
"gnomad_genomes_af": 0.0000131409,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4000000059604645,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9359999895095825,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.957,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.98,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999981760802075,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Moderate,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000297.4",
"gene_symbol": "PKD2",
"hgnc_id": 9009,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1319+1G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal dominant polycystic kidney disease,Inborn genetic diseases,Polycystic kidney disease,Polycystic kidney disease 2,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:9 LP:2",
"phenotype_combined": "Polycystic kidney disease 2|Autosomal dominant polycystic kidney disease|Inborn genetic diseases|not provided|Polycystic kidney disease",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}