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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: 10-101010781-CT-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=101010781&ref=CT&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 101010781,
"ref": "CT",
"alt": "C",
"effect": "frameshift_variant",
"transcript": "ENST00000619208.6",
"consequences": [
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.2107delA",
"hgvs_p": "p.Ser703fs",
"transcript": "NM_001195263.2",
"protein_id": "NP_001182192.1",
"transcript_support_level": null,
"aa_start": 703,
"aa_end": null,
"aa_length": 1033,
"cds_start": 2107,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 2329,
"cdna_end": null,
"cdna_length": 4112,
"mane_select": "ENST00000619208.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.2107delA",
"hgvs_p": "p.Ser703fs",
"transcript": "ENST00000619208.6",
"protein_id": "ENSP00000480489.1",
"transcript_support_level": 5,
"aa_start": 703,
"aa_end": null,
"aa_length": 1033,
"cds_start": 2107,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 2329,
"cdna_end": null,
"cdna_length": 4112,
"mane_select": "NM_001195263.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.2104delA",
"hgvs_p": "p.Ser702fs",
"transcript": "NM_001437429.1",
"protein_id": "NP_001424358.1",
"transcript_support_level": null,
"aa_start": 702,
"aa_end": null,
"aa_length": 1032,
"cds_start": 2104,
"cds_end": null,
"cds_length": 3099,
"cdna_start": 2326,
"cdna_end": null,
"cdna_length": 4109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.2107delA",
"hgvs_p": "p.Ser703fs",
"transcript": "XM_011540177.4",
"protein_id": "XP_011538479.1",
"transcript_support_level": null,
"aa_start": 703,
"aa_end": null,
"aa_length": 1033,
"cds_start": 2107,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 2502,
"cdna_end": null,
"cdna_length": 4285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.2107delA",
"hgvs_p": "p.Ser703fs",
"transcript": "XM_047425767.1",
"protein_id": "XP_047281723.1",
"transcript_support_level": null,
"aa_start": 703,
"aa_end": null,
"aa_length": 1033,
"cds_start": 2107,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 2890,
"cdna_end": null,
"cdna_length": 4673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "n.*2054delA",
"hgvs_p": null,
"transcript": "ENST00000474125.7",
"protein_id": "ENSP00000474447.1",
"transcript_support_level": 2,
"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": 4306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "n.*2054delA",
"hgvs_p": null,
"transcript": "ENST00000474125.7",
"protein_id": "ENSP00000474447.1",
"transcript_support_level": 2,
"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": 4306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.*69delA",
"hgvs_p": null,
"transcript": "XM_011540179.4",
"protein_id": "XP_011538481.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 677,
"cds_start": -4,
"cds_end": null,
"cds_length": 2034,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"dbsnp": "rs397516633",
"frequency_reference_population": 0.00044869975,
"hom_count_reference_population": 2,
"allele_count_reference_population": 689,
"gnomad_exomes_af": 0.000468441,
"gnomad_genomes_af": 0.000269319,
"gnomad_exomes_ac": 648,
"gnomad_genomes_ac": 41,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.04,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1,PP5,BS2_Supporting",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 1,
"pathogenic_score": 9,
"criteria": [
"PVS1",
"PP5",
"BS2_Supporting"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000619208.6",
"gene_symbol": "PDZD7",
"hgnc_id": 26257,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.2107delA",
"hgvs_p": "p.Ser703fs"
}
],
"clinvar_disease": " GPR98/PDZD7 digenic, autosomal recessive 57, type IIC,Hearing loss,PDZD7-related disorder,Retinal dystrophy,Usher syndrome,Usher syndrome type 2A,Usher syndrome type 2C,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:4 LP:2 US:1",
"phenotype_combined": "Hearing loss, autosomal recessive 57|not provided|Usher syndrome, type IIC, GPR98/PDZD7 digenic|Retinal dystrophy|Usher syndrome type 2C;Usher syndrome type 2A;Hearing loss, autosomal recessive 57|PDZD7-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}