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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: 2-32250616-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=32250616&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 32250616,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000402280.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLRC4",
"gene_hgnc_id": 16412,
"hgvs_c": "c.1248G>A",
"hgvs_p": "p.Val416Val",
"transcript": "NM_001199138.2",
"protein_id": "NP_001186067.1",
"transcript_support_level": null,
"aa_start": 416,
"aa_end": null,
"aa_length": 1024,
"cds_start": 1248,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 1515,
"cdna_end": null,
"cdna_length": 3362,
"mane_select": "ENST00000402280.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLRC4",
"gene_hgnc_id": 16412,
"hgvs_c": "c.1248G>A",
"hgvs_p": "p.Val416Val",
"transcript": "ENST00000402280.6",
"protein_id": "ENSP00000385428.1",
"transcript_support_level": 1,
"aa_start": 416,
"aa_end": null,
"aa_length": 1024,
"cds_start": 1248,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 1515,
"cdna_end": null,
"cdna_length": 3362,
"mane_select": "NM_001199138.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLRC4",
"gene_hgnc_id": 16412,
"hgvs_c": "c.1248G>A",
"hgvs_p": "p.Val416Val",
"transcript": "ENST00000360906.9",
"protein_id": "ENSP00000354159.5",
"transcript_support_level": 1,
"aa_start": 416,
"aa_end": null,
"aa_length": 1024,
"cds_start": 1248,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 1512,
"cdna_end": null,
"cdna_length": 3359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NLRC4",
"gene_hgnc_id": 16412,
"hgvs_c": "c.262+1803G>A",
"hgvs_p": null,
"transcript": "ENST00000342905.10",
"protein_id": "ENSP00000339666.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 359,
"cds_start": -4,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1362,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLRC4",
"gene_hgnc_id": 16412,
"hgvs_c": "c.1248G>A",
"hgvs_p": "p.Val416Val",
"transcript": "NM_001199139.1",
"protein_id": "NP_001186068.1",
"transcript_support_level": null,
"aa_start": 416,
"aa_end": null,
"aa_length": 1024,
"cds_start": 1248,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 1392,
"cdna_end": null,
"cdna_length": 3243,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLRC4",
"gene_hgnc_id": 16412,
"hgvs_c": "c.1248G>A",
"hgvs_p": "p.Val416Val",
"transcript": "NM_021209.4",
"protein_id": "NP_067032.3",
"transcript_support_level": null,
"aa_start": 416,
"aa_end": null,
"aa_length": 1024,
"cds_start": 1248,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 1523,
"cdna_end": null,
"cdna_length": 3374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLRC4",
"gene_hgnc_id": 16412,
"hgvs_c": "c.1248G>A",
"hgvs_p": "p.Val416Val",
"transcript": "XM_047445356.1",
"protein_id": "XP_047301312.1",
"transcript_support_level": null,
"aa_start": 416,
"aa_end": null,
"aa_length": 756,
"cds_start": 1248,
"cds_end": null,
"cds_length": 2271,
"cdna_start": 1515,
"cdna_end": null,
"cdna_length": 2622,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLRC4",
"gene_hgnc_id": 16412,
"hgvs_c": "n.1248G>A",
"hgvs_p": null,
"transcript": "ENST00000404025.3",
"protein_id": "ENSP00000385090.3",
"transcript_support_level": 5,
"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": 3416,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289727",
"gene_hgnc_id": null,
"hgvs_c": "n.1245C>T",
"hgvs_p": null,
"transcript": "ENST00000697333.1",
"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": 2581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NLRC4",
"gene_hgnc_id": 16412,
"hgvs_c": "c.262+1803G>A",
"hgvs_p": null,
"transcript": "NM_001302504.1",
"protein_id": "NP_001289433.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 359,
"cds_start": -4,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NLRC4",
"gene_hgnc_id": 16412,
"hgvs_c": "c.-76+6159G>A",
"hgvs_p": null,
"transcript": "ENST00000652197.2",
"protein_id": "ENSP00000498301.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 255,
"cds_start": -4,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289727",
"gene_hgnc_id": null,
"hgvs_c": "n.2994-2719C>T",
"hgvs_p": null,
"transcript": "ENST00000697331.1",
"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": 3467,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289727",
"gene_hgnc_id": null,
"hgvs_c": "n.2977+14238C>T",
"hgvs_p": null,
"transcript": "ENST00000697332.1",
"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": 3261,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NLRC4",
"gene_hgnc_id": 16412,
"dbsnp": "rs377140938",
"frequency_reference_population": 0.0008611247,
"hom_count_reference_population": 3,
"allele_count_reference_population": 1390,
"gnomad_exomes_af": 0.000877666,
"gnomad_genomes_af": 0.000702395,
"gnomad_exomes_ac": 1283,
"gnomad_genomes_ac": 107,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6899999976158142,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.417,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000402280.6",
"gene_symbol": "NLRC4",
"hgnc_id": 16412,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1248G>A",
"hgvs_p": "p.Val416Val"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000697333.1",
"gene_symbol": "ENSG00000289727",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1245C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Autoinflammatory syndrome,Familial cold autoinflammatory syndrome 4,Periodic fever-infantile enterocolitis-autoinflammatory syndrome,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:2",
"phenotype_combined": "Familial cold autoinflammatory syndrome 4;Periodic fever-infantile enterocolitis-autoinflammatory syndrome|not provided|Autoinflammatory syndrome|not specified",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}