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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: 10-117543426-G-GGCC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=117543426&ref=G&alt=GGCC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 117543426,
"ref": "G",
"alt": "GGCC",
"effect": "disruptive_inframe_insertion",
"transcript": "NM_004098.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "AG",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMX2",
"gene_hgnc_id": 3341,
"hgvs_c": "c.176_178dupCCG",
"hgvs_p": "p.Ala59dup",
"transcript": "NM_004098.4",
"protein_id": "NP_004089.1",
"transcript_support_level": null,
"aa_start": 60,
"aa_end": null,
"aa_length": 252,
"cds_start": 179,
"cds_end": null,
"cds_length": 759,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000553456.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004098.4"
},
{
"aa_ref": "G",
"aa_alt": "AG",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMX2",
"gene_hgnc_id": 3341,
"hgvs_c": "c.176_178dupCCG",
"hgvs_p": "p.Ala59dup",
"transcript": "ENST00000553456.5",
"protein_id": "ENSP00000450962.3",
"transcript_support_level": 1,
"aa_start": 60,
"aa_end": null,
"aa_length": 252,
"cds_start": 179,
"cds_end": null,
"cds_length": 759,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004098.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000553456.5"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "EMX2OS",
"gene_hgnc_id": 18511,
"hgvs_c": "n.574+877_574+879dupGGC",
"hgvs_p": null,
"transcript": "ENST00000551288.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000551288.5"
},
{
"aa_ref": "G",
"aa_alt": "AG",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMX2",
"gene_hgnc_id": 3341,
"hgvs_c": "c.176_178dupCCG",
"hgvs_p": "p.Ala59dup",
"transcript": "NM_001165924.2",
"protein_id": "NP_001159396.1",
"transcript_support_level": null,
"aa_start": 60,
"aa_end": null,
"aa_length": 169,
"cds_start": 179,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001165924.2"
},
{
"aa_ref": "G",
"aa_alt": "AG",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMX2",
"gene_hgnc_id": 3341,
"hgvs_c": "c.176_178dupCCG",
"hgvs_p": "p.Ala59dup",
"transcript": "ENST00000442245.5",
"protein_id": "ENSP00000474874.1",
"transcript_support_level": 2,
"aa_start": 60,
"aa_end": null,
"aa_length": 169,
"cds_start": 179,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000442245.5"
},
{
"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": "EMX2OS",
"gene_hgnc_id": 18511,
"hgvs_c": "n.93+220_93+222dupGGC",
"hgvs_p": null,
"transcript": "ENST00000748259.1",
"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": "ENST00000748259.1"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "EMX2OS",
"gene_hgnc_id": 18511,
"hgvs_c": "n.574+877_574+879dupGGC",
"hgvs_p": null,
"transcript": "NR_002791.2",
"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_002791.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMX2",
"gene_hgnc_id": 3341,
"hgvs_c": "c.-142_-141insGCC",
"hgvs_p": null,
"transcript": "ENST00000616794.1",
"protein_id": "ENSP00000480271.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 69,
"cds_start": null,
"cds_end": null,
"cds_length": 210,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000616794.1"
}
],
"gene_symbol": "EMX2",
"gene_hgnc_id": 3341,
"dbsnp": "rs756693906",
"frequency_reference_population": 0.000053830678,
"hom_count_reference_population": 0,
"allele_count_reference_population": 86,
"gnomad_exomes_af": 0.0000553338,
"gnomad_genomes_af": 0.0000395179,
"gnomad_exomes_ac": 80,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"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": 3.7,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP3,BP6,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP3",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_004098.4",
"gene_symbol": "EMX2",
"hgnc_id": 3341,
"effects": [
"disruptive_inframe_insertion"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.176_178dupCCG",
"hgvs_p": "p.Ala59dup"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000551288.5",
"gene_symbol": "EMX2OS",
"hgnc_id": 18511,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.574+877_574+879dupGGC",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}