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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: 2-88590826-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=88590826&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 88590826,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000303236.9",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "c.994G>T",
"hgvs_p": "p.Glu332*",
"transcript": "NM_004836.7",
"protein_id": "NP_004827.4",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 1116,
"cds_start": 994,
"cds_end": null,
"cds_length": 3351,
"cdna_start": 1184,
"cdna_end": null,
"cdna_length": 4536,
"mane_select": "ENST00000303236.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "c.994G>T",
"hgvs_p": "p.Glu332*",
"transcript": "ENST00000303236.9",
"protein_id": "ENSP00000307235.3",
"transcript_support_level": 1,
"aa_start": 332,
"aa_end": null,
"aa_length": 1116,
"cds_start": 994,
"cds_end": null,
"cds_length": 3351,
"cdna_start": 1184,
"cdna_end": null,
"cdna_length": 4536,
"mane_select": "NM_004836.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "n.663G>T",
"hgvs_p": null,
"transcript": "ENST00000415570.1",
"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": 2902,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "c.541G>T",
"hgvs_p": "p.Glu181*",
"transcript": "NM_001313915.2",
"protein_id": "NP_001300844.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 965,
"cds_start": 541,
"cds_end": null,
"cds_length": 2898,
"cdna_start": 870,
"cdna_end": null,
"cdna_length": 4222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "c.541G>T",
"hgvs_p": "p.Glu181*",
"transcript": "ENST00000682892.1",
"protein_id": "ENSP00000507214.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 965,
"cds_start": 541,
"cds_end": null,
"cds_length": 2898,
"cdna_start": 1572,
"cdna_end": null,
"cdna_length": 4724,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "c.391G>T",
"hgvs_p": "p.Glu131*",
"transcript": "ENST00000684642.1",
"protein_id": "ENSP00000507355.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 859,
"cds_start": 391,
"cds_end": null,
"cds_length": 2580,
"cdna_start": 391,
"cdna_end": null,
"cdna_length": 3547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "c.703G>T",
"hgvs_p": "p.Glu235*",
"transcript": "XM_047446428.1",
"protein_id": "XP_047302384.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 1019,
"cds_start": 703,
"cds_end": null,
"cds_length": 3060,
"cdna_start": 1143,
"cdna_end": null,
"cdna_length": 4495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "c.310G>T",
"hgvs_p": "p.Glu104*",
"transcript": "XM_047446429.1",
"protein_id": "XP_047302385.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 888,
"cds_start": 310,
"cds_end": null,
"cds_length": 2667,
"cdna_start": 507,
"cdna_end": null,
"cdna_length": 3859,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "c.994G>T",
"hgvs_p": "p.Glu332*",
"transcript": "XM_047446430.1",
"protein_id": "XP_047302386.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 614,
"cds_start": 994,
"cds_end": null,
"cds_length": 1845,
"cdna_start": 1184,
"cdna_end": null,
"cdna_length": 2138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "n.*512G>T",
"hgvs_p": null,
"transcript": "ENST00000652099.1",
"protein_id": "ENSP00000498211.1",
"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": 4346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "n.870G>T",
"hgvs_p": null,
"transcript": "ENST00000652736.1",
"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": 4222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "n.2185G>T",
"hgvs_p": null,
"transcript": "ENST00000681996.1",
"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": 2425,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "n.449G>T",
"hgvs_p": null,
"transcript": "ENST00000682276.1",
"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": 3722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "n.633G>T",
"hgvs_p": null,
"transcript": "ENST00000682952.1",
"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": 3916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "n.*155G>T",
"hgvs_p": null,
"transcript": "ENST00000684455.1",
"protein_id": "ENSP00000506923.1",
"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": 3490,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "n.*512G>T",
"hgvs_p": null,
"transcript": "ENST00000652099.1",
"protein_id": "ENSP00000498211.1",
"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": 4346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"hgvs_c": "n.*155G>T",
"hgvs_p": null,
"transcript": "ENST00000684455.1",
"protein_id": "ENSP00000506923.1",
"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": 3490,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EIF2AK3",
"gene_hgnc_id": 3255,
"dbsnp": "rs121908570",
"frequency_reference_population": 0.0000013682867,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136829,
"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": 0.6499999761581421,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.65,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.284,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.07,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000303236.9",
"gene_symbol": "EIF2AK3",
"hgnc_id": 3255,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.994G>T",
"hgvs_p": "p.Glu332*"
}
],
"clinvar_disease": "Wolcott-Rallison dysplasia",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Wolcott-Rallison dysplasia",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}