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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: 16-68829651-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=68829651&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"PP5",
"BP4"
],
"effects": [
"splice_region_variant",
"intron_variant"
],
"gene_symbol": "CDH1",
"hgnc_id": 1748,
"hgvs_c": "c.2296-3A>G",
"hgvs_p": null,
"inheritance_mode": "Unknown,AD",
"pathogenic_score": 3,
"score": 2,
"transcript": "NM_004360.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP5,BP4",
"acmg_score": 2,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.35,
"chr": "16",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Hereditary cancer-predisposing syndrome,Hereditary diffuse gastric adenocarcinoma,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:3 US:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.3499999940395355,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 882,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4811,
"cdna_start": null,
"cds_end": null,
"cds_length": 2649,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_004360.5",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "c.2296-3A>G",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000261769.10",
"protein_coding": true,
"protein_id": "NP_004351.1",
"strand": true,
"transcript": "NM_004360.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 882,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4811,
"cdna_start": null,
"cds_end": null,
"cds_length": 2649,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000261769.10",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "c.2296-3A>G",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004360.5",
"protein_coding": true,
"protein_id": "ENSP00000261769.4",
"strand": true,
"transcript": "ENST00000261769.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 821,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2567,
"cdna_start": null,
"cds_end": null,
"cds_length": 2466,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000422392.6",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "c.2113-3A>G",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000414946.2",
"strand": true,
"transcript": "ENST00000422392.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2759,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000562836.5",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "n.2367-3A>G",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000562836.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4138,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000566612.5",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "n.*536-3A>G",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000454782.1",
"strand": true,
"transcript": "ENST00000566612.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 834,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4667,
"cdna_start": null,
"cds_end": null,
"cds_length": 2505,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000931199.1",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "c.2295+1347A>G",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601258.1",
"strand": true,
"transcript": "ENST00000931199.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 821,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4628,
"cdna_start": null,
"cds_end": null,
"cds_length": 2466,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001317184.2",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "c.2113-3A>G",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001304113.1",
"strand": true,
"transcript": "NM_001317184.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 806,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4586,
"cdna_start": null,
"cds_end": null,
"cds_length": 2421,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000884375.1",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "c.2068-3A>G",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554434.1",
"strand": true,
"transcript": "ENST00000884375.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 366,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4878,
"cdna_start": null,
"cds_end": null,
"cds_length": 1101,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001317185.2",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "c.748-3A>G",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001304114.1",
"strand": true,
"transcript": "NM_001317185.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 227,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4665,
"cdna_start": null,
"cds_end": null,
"cds_length": 684,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001317186.2",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "c.331-3A>G",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001304115.1",
"strand": true,
"transcript": "NM_001317186.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 952,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000562118.1",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "n.514-3A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000562118.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2661,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000566510.5",
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"hgvs_c": "n.*962-3A>G",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000458139.1",
"strand": true,
"transcript": "ENST00000566510.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.325147526980657,
"dbsnp": "rs113067020",
"effect": "splice_region_variant,intron_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 1748,
"gene_symbol": "CDH1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not provided|Hereditary diffuse gastric adenocarcinoma|not specified|Hereditary cancer-predisposing syndrome",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.392,
"pos": 68829651,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.3540000021457672,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 1,
"transcript": "NM_004360.5"
}
]
}