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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: 5-35876172-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=35876172&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 35876172,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_002185.5",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"hgvs_c": "c.1066A>G",
"hgvs_p": "p.Ile356Val",
"transcript": "NM_002185.5",
"protein_id": "NP_002176.2",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 459,
"cds_start": 1066,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000303115.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002185.5"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"hgvs_c": "c.1066A>G",
"hgvs_p": "p.Ile356Val",
"transcript": "ENST00000303115.8",
"protein_id": "ENSP00000306157.3",
"transcript_support_level": 1,
"aa_start": 356,
"aa_end": null,
"aa_length": 459,
"cds_start": 1066,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002185.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000303115.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"hgvs_c": "c.*564A>G",
"hgvs_p": null,
"transcript": "NM_001437964.1",
"protein_id": "NP_001424893.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 298,
"cds_start": null,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001437964.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"hgvs_c": "c.*183A>G",
"hgvs_p": null,
"transcript": "NM_001410734.1",
"protein_id": "NP_001397663.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 262,
"cds_start": null,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001410734.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"hgvs_c": "c.*581A>G",
"hgvs_p": null,
"transcript": "NM_001437963.1",
"protein_id": "NP_001424892.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 261,
"cds_start": null,
"cds_end": null,
"cds_length": 786,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001437963.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"hgvs_c": "c.*183A>G",
"hgvs_p": null,
"transcript": "ENST00000505093.1",
"protein_id": "ENSP00000426069.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 65,
"cds_start": null,
"cds_end": null,
"cds_length": 198,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000505093.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"hgvs_c": "c.783-92A>G",
"hgvs_p": null,
"transcript": "ENST00000877114.1",
"protein_id": "ENSP00000547173.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 334,
"cds_start": null,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877114.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"hgvs_c": "n.364A>G",
"hgvs_p": null,
"transcript": "ENST00000505875.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000505875.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"hgvs_c": "n.*260A>G",
"hgvs_p": null,
"transcript": "ENST00000514217.5",
"protein_id": "ENSP00000427688.1",
"transcript_support_level": 2,
"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": "nonsense_mediated_decay",
"feature": "ENST00000514217.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"hgvs_c": "n.890A>G",
"hgvs_p": null,
"transcript": "NR_120485.3",
"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_120485.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"hgvs_c": "n.*260A>G",
"hgvs_p": null,
"transcript": "ENST00000514217.5",
"protein_id": "ENSP00000427688.1",
"transcript_support_level": 2,
"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": "nonsense_mediated_decay",
"feature": "ENST00000514217.5"
}
],
"gene_symbol": "IL7R",
"gene_hgnc_id": 6024,
"dbsnp": "rs3194051",
"frequency_reference_population": 0.25656244,
"hom_count_reference_population": 55069,
"allele_count_reference_population": 414023,
"gnomad_exomes_af": 0.254455,
"gnomad_genomes_af": 0.27683,
"gnomad_exomes_ac": 371947,
"gnomad_genomes_ac": 42076,
"gnomad_exomes_homalt": 48910,
"gnomad_genomes_homalt": 6159,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004357248544692993,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.019,
"revel_prediction": "Benign",
"alphamissense_score": 0.0693,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.065,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BA1,BS2_Supporting",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BA1",
"BS2_Supporting"
],
"verdict": "Benign",
"transcript": "NM_002185.5",
"gene_symbol": "IL7R",
"hgnc_id": 6024,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1066A>G",
"hgvs_p": "p.Ile356Val"
}
],
"clinvar_disease": "Immunodeficiency 104,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "B:7 O:2",
"phenotype_combined": "not specified|Immunodeficiency 104|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}