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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: 16-68822061-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=68822061&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 68822061,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000261769.10",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.1772A>G",
"hgvs_p": "p.Asn591Ser",
"transcript": "NM_004360.5",
"protein_id": "NP_004351.1",
"transcript_support_level": null,
"aa_start": 591,
"aa_end": null,
"aa_length": 882,
"cds_start": 1772,
"cds_end": null,
"cds_length": 2649,
"cdna_start": 1896,
"cdna_end": null,
"cdna_length": 4811,
"mane_select": "ENST00000261769.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.1772A>G",
"hgvs_p": "p.Asn591Ser",
"transcript": "ENST00000261769.10",
"protein_id": "ENSP00000261769.4",
"transcript_support_level": 1,
"aa_start": 591,
"aa_end": null,
"aa_length": 882,
"cds_start": 1772,
"cds_end": null,
"cds_length": 2649,
"cdna_start": 1896,
"cdna_end": null,
"cdna_length": 4811,
"mane_select": "NM_004360.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.1589A>G",
"hgvs_p": "p.Asn530Ser",
"transcript": "ENST00000422392.6",
"protein_id": "ENSP00000414946.2",
"transcript_support_level": 1,
"aa_start": 530,
"aa_end": null,
"aa_length": 821,
"cds_start": 1589,
"cds_end": null,
"cds_length": 2466,
"cdna_start": 1653,
"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": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "n.1843A>G",
"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": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "n.*12A>G",
"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": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "n.*12A>G",
"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": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.1589A>G",
"hgvs_p": "p.Asn530Ser",
"transcript": "NM_001317184.2",
"protein_id": "NP_001304113.1",
"transcript_support_level": null,
"aa_start": 530,
"aa_end": null,
"aa_length": 821,
"cds_start": 1589,
"cds_end": null,
"cds_length": 2466,
"cdna_start": 1713,
"cdna_end": null,
"cdna_length": 4628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.224A>G",
"hgvs_p": "p.Asn75Ser",
"transcript": "NM_001317185.2",
"protein_id": "NP_001304114.1",
"transcript_support_level": null,
"aa_start": 75,
"aa_end": null,
"aa_length": 366,
"cds_start": 224,
"cds_end": null,
"cds_length": 1101,
"cdna_start": 1963,
"cdna_end": null,
"cdna_length": 4878,
"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": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "n.*438A>G",
"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": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "c.-194A>G",
"hgvs_p": null,
"transcript": "NM_001317186.2",
"protein_id": "NP_001304115.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 227,
"cds_start": -4,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"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": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH1",
"gene_hgnc_id": 1748,
"hgvs_c": "n.*438A>G",
"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": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000260798",
"gene_hgnc_id": null,
"hgvs_c": "n.263+1203T>C",
"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": "rs1555516835",
"frequency_reference_population": 0.0000013680957,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.0000013681,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8341050744056702,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.351,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2548,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.576,
"phylop100way_prediction": "Pathogenic",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000261769.10",
"gene_symbol": "CDH1",
"hgnc_id": 1748,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1772A>G",
"hgvs_p": "p.Asn591Ser"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000563916.1",
"gene_symbol": "ENSG00000260798",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.263+1203T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Familial cancer of breast,Hereditary cancer-predisposing syndrome,Hereditary diffuse gastric adenocarcinoma,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"phenotype_combined": "Familial cancer of breast|Hereditary diffuse gastric adenocarcinoma|Hereditary cancer-predisposing syndrome|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}