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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: 16-68823536-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=68823536&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 68823536,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000261769.10",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.2074G>A",
"hgvs_p": "p.Ala692Thr",
"transcript": "NM_004360.5",
"protein_id": "NP_004351.1",
"transcript_support_level": null,
"aa_start": 692,
"aa_end": null,
"aa_length": 882,
"cds_start": 2074,
"cds_end": null,
"cds_length": 2649,
"cdna_start": 2198,
"cdna_end": null,
"cdna_length": 4811,
"mane_select": "ENST00000261769.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.2074G>A",
"hgvs_p": "p.Ala692Thr",
"transcript": "ENST00000261769.10",
"protein_id": "ENSP00000261769.4",
"transcript_support_level": 1,
"aa_start": 692,
"aa_end": null,
"aa_length": 882,
"cds_start": 2074,
"cds_end": null,
"cds_length": 2649,
"cdna_start": 2198,
"cdna_end": null,
"cdna_length": 4811,
"mane_select": "NM_004360.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.1891G>A",
"hgvs_p": "p.Ala631Thr",
"transcript": "ENST00000422392.6",
"protein_id": "ENSP00000414946.2",
"transcript_support_level": 1,
"aa_start": 631,
"aa_end": null,
"aa_length": 821,
"cds_start": 1891,
"cds_end": null,
"cds_length": 2466,
"cdna_start": 1955,
"cdna_end": null,
"cdna_length": 2567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "n.2145G>A",
"hgvs_p": null,
"transcript": "ENST00000562836.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "n.*314G>A",
"hgvs_p": null,
"transcript": "ENST00000566612.5",
"protein_id": "ENSP00000454782.1",
"transcript_support_level": 1,
"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": 4138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "n.*314G>A",
"hgvs_p": null,
"transcript": "ENST00000566612.5",
"protein_id": "ENSP00000454782.1",
"transcript_support_level": 1,
"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": 4138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.1891G>A",
"hgvs_p": "p.Ala631Thr",
"transcript": "NM_001317184.2",
"protein_id": "NP_001304113.1",
"transcript_support_level": null,
"aa_start": 631,
"aa_end": null,
"aa_length": 821,
"cds_start": 1891,
"cds_end": null,
"cds_length": 2466,
"cdna_start": 2015,
"cdna_end": null,
"cdna_length": 4628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.526G>A",
"hgvs_p": "p.Ala176Thr",
"transcript": "NM_001317185.2",
"protein_id": "NP_001304114.1",
"transcript_support_level": null,
"aa_start": 176,
"aa_end": null,
"aa_length": 366,
"cds_start": 526,
"cds_end": null,
"cds_length": 1101,
"cdna_start": 2265,
"cdna_end": null,
"cdna_length": 4878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Ala37Thr",
"transcript": "NM_001317186.2",
"protein_id": "NP_001304115.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 227,
"cds_start": 109,
"cds_end": null,
"cds_length": 684,
"cdna_start": 2052,
"cdna_end": null,
"cdna_length": 4665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "n.292G>A",
"hgvs_p": null,
"transcript": "ENST00000562118.1",
"protein_id": null,
"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": 952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "n.*740G>A",
"hgvs_p": null,
"transcript": "ENST00000566510.5",
"protein_id": "ENSP00000458139.1",
"transcript_support_level": 5,
"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": 2661,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "n.*740G>A",
"hgvs_p": null,
"transcript": "ENST00000566510.5",
"protein_id": "ENSP00000458139.1",
"transcript_support_level": 5,
"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": 2661,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000260798",
"gene_hgnc_id": null,
"hgvs_c": "n.-10C>T",
"hgvs_p": null,
"transcript": "ENST00000563916.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"dbsnp": "rs376854556",
"frequency_reference_population": 0.000015490965,
"hom_count_reference_population": 0,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.0000136823,
"gnomad_genomes_af": 0.0000328722,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10626214742660522,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.106,
"revel_prediction": "Benign",
"alphamissense_score": 0.0742,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.27,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2_Supporting",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000261769.10",
"gene_symbol": "CDH1",
"hgnc_id": 1748,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2074G>A",
"hgvs_p": "p.Ala692Thr"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000563916.1",
"gene_symbol": "ENSG00000260798",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-10C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Familial cancer of breast,Hereditary cancer-predisposing syndrome,Hereditary diffuse gastric adenocarcinoma,Ovarian cancer,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:5 LB:1 O:2",
"phenotype_combined": "not specified|Hereditary diffuse gastric adenocarcinoma|Hereditary cancer-predisposing syndrome|not provided|Ovarian cancer;Familial cancer of breast",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}