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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: 1-47416772-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=47416772&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 47416772,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000335071.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXE3",
"gene_hgnc_id": 3808,
"hgvs_c": "c.457G>C",
"hgvs_p": "p.Asp153His",
"transcript": "NM_012186.3",
"protein_id": "NP_036318.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 319,
"cds_start": 457,
"cds_end": null,
"cds_length": 960,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 1768,
"mane_select": "ENST00000335071.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FOXE3",
"gene_hgnc_id": 3808,
"hgvs_c": "c.457G>C",
"hgvs_p": "p.Asp153His",
"transcript": "ENST00000335071.4",
"protein_id": "ENSP00000334472.2",
"transcript_support_level": 6,
"aa_start": 153,
"aa_end": null,
"aa_length": 319,
"cds_start": 457,
"cds_end": null,
"cds_length": 960,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 1768,
"mane_select": "NM_012186.3",
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LINC01389",
"gene_hgnc_id": 50661,
"hgvs_c": "n.207+16591C>G",
"hgvs_p": null,
"transcript": "ENST00000828805.1",
"protein_id": null,
"transcript_support_level": null,
"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": 555,
"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": "LINC01389",
"gene_hgnc_id": 50661,
"hgvs_c": "n.92+459C>G",
"hgvs_p": null,
"transcript": "ENST00000828806.1",
"protein_id": null,
"transcript_support_level": null,
"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": 552,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LINC01389",
"gene_hgnc_id": 50661,
"hgvs_c": "n.92+459C>G",
"hgvs_p": null,
"transcript": "ENST00000828807.1",
"protein_id": null,
"transcript_support_level": null,
"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": 816,
"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": "LINC01389",
"gene_hgnc_id": 50661,
"hgvs_c": "n.81+459C>G",
"hgvs_p": null,
"transcript": "ENST00000828808.1",
"protein_id": null,
"transcript_support_level": null,
"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": 588,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LINC01389",
"gene_hgnc_id": 50661,
"hgvs_c": "n.81+459C>G",
"hgvs_p": null,
"transcript": "ENST00000828809.1",
"protein_id": null,
"transcript_support_level": null,
"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": 430,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LINC01389",
"gene_hgnc_id": 50661,
"hgvs_c": "n.49+459C>G",
"hgvs_p": null,
"transcript": "ENST00000828810.1",
"protein_id": null,
"transcript_support_level": null,
"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": 696,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LINC01389",
"gene_hgnc_id": 50661,
"hgvs_c": "n.41+459C>G",
"hgvs_p": null,
"transcript": "ENST00000828811.1",
"protein_id": null,
"transcript_support_level": null,
"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": 654,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LINC01389",
"gene_hgnc_id": 50661,
"hgvs_c": "n.29-6871C>G",
"hgvs_p": null,
"transcript": "NR_126355.1",
"protein_id": null,
"transcript_support_level": null,
"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": 861,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FOXE3",
"gene_hgnc_id": 3808,
"dbsnp": "rs367943249",
"frequency_reference_population": 0.000010627258,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.00000621132,
"gnomad_genomes_af": 0.0000530884,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9255558252334595,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.624,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9609,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.786,
"phylop100way_prediction": "Benign",
"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": "PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000335071.4",
"gene_symbol": "FOXE3",
"hgnc_id": 3808,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.457G>C",
"hgvs_p": "p.Asp153His"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NR_126355.1",
"gene_symbol": "LINC01389",
"hgnc_id": 50661,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.29-6871C>G",
"hgvs_p": null
}
],
"clinvar_disease": " familial thoracic 11, susceptibility to,Acute aortic dissection,Anterior segment dysgenesis,Aortic aneurysm,Cardiovascular phenotype,Congenital aneurysm of ascending aorta,Congenital primary aphakia",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:1",
"phenotype_combined": "Aortic aneurysm, familial thoracic 11, susceptibility to|Congenital aneurysm of ascending aorta;Acute aortic dissection|Congenital primary aphakia;Anterior segment dysgenesis|Cardiovascular phenotype",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}