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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: 15-40008067-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=40008067&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 40008067,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000263791.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK4",
"gene_hgnc_id": 19687,
"hgvs_c": "c.3448C>T",
"hgvs_p": "p.Arg1150*",
"transcript": "NM_001013703.4",
"protein_id": "NP_001013725.2",
"transcript_support_level": null,
"aa_start": 1150,
"aa_end": null,
"aa_length": 1649,
"cds_start": 3448,
"cds_end": null,
"cds_length": 4950,
"cdna_start": 3529,
"cdna_end": null,
"cdna_length": 5538,
"mane_select": "ENST00000263791.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK4",
"gene_hgnc_id": 19687,
"hgvs_c": "c.3448C>T",
"hgvs_p": "p.Arg1150*",
"transcript": "ENST00000263791.10",
"protein_id": "ENSP00000263791.5",
"transcript_support_level": 2,
"aa_start": 1150,
"aa_end": null,
"aa_length": 1649,
"cds_start": 3448,
"cds_end": null,
"cds_length": 4950,
"cdna_start": 3529,
"cdna_end": null,
"cdna_length": 5538,
"mane_select": "NM_001013703.4",
"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": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK4",
"gene_hgnc_id": 19687,
"hgvs_c": "n.2365C>T",
"hgvs_p": null,
"transcript": "ENST00000558629.5",
"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": 4374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK4",
"gene_hgnc_id": 19687,
"hgvs_c": "c.2779C>T",
"hgvs_p": "p.Arg927*",
"transcript": "ENST00000560855.5",
"protein_id": "ENSP00000453575.1",
"transcript_support_level": 5,
"aa_start": 927,
"aa_end": null,
"aa_length": 1426,
"cds_start": 2779,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 2780,
"cdna_end": null,
"cdna_length": 4789,
"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": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK4",
"gene_hgnc_id": 19687,
"hgvs_c": "n.611C>T",
"hgvs_p": null,
"transcript": "ENST00000558557.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 2449,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2AK4",
"gene_hgnc_id": 19687,
"hgvs_c": "n.409C>T",
"hgvs_p": null,
"transcript": "ENST00000559311.5",
"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": 535,
"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": "ENSG00000306490",
"gene_hgnc_id": null,
"hgvs_c": "n.196-9179G>A",
"hgvs_p": null,
"transcript": "ENST00000819059.1",
"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": 466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EIF2AK4",
"gene_hgnc_id": 19687,
"dbsnp": "rs587777208",
"frequency_reference_population": 0.0000031052468,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000274351,
"gnomad_genomes_af": 0.00000657073,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6600000262260437,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.44999998807907104,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.66,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.715,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.45,
"spliceai_max_prediction": "Uncertain_significance",
"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": "ENST00000263791.10",
"gene_symbol": "EIF2AK4",
"hgnc_id": 19687,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.3448C>T",
"hgvs_p": "p.Arg1150*"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000819059.1",
"gene_symbol": "ENSG00000306490",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.196-9179G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Familial pulmonary capillary hemangiomatosis",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Familial pulmonary capillary hemangiomatosis",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}