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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: 5-1878357-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=1878357&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 1878357,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000231357.7",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "c.1172C>T",
"hgvs_p": "p.Pro391Leu",
"transcript": "NM_016358.3",
"protein_id": "NP_057442.1",
"transcript_support_level": null,
"aa_start": 391,
"aa_end": null,
"aa_length": 519,
"cds_start": 1172,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 1450,
"cdna_end": null,
"cdna_length": 2394,
"mane_select": "ENST00000231357.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "c.1172C>T",
"hgvs_p": "p.Pro391Leu",
"transcript": "ENST00000231357.7",
"protein_id": "ENSP00000231357.2",
"transcript_support_level": 1,
"aa_start": 391,
"aa_end": null,
"aa_length": 519,
"cds_start": 1172,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 1450,
"cdna_end": null,
"cdna_length": 2394,
"mane_select": "NM_016358.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "c.1172C>T",
"hgvs_p": "p.Pro391Leu",
"transcript": "ENST00000505790.5",
"protein_id": "ENSP00000423161.1",
"transcript_support_level": 1,
"aa_start": 391,
"aa_end": null,
"aa_length": 519,
"cds_start": 1172,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 1629,
"cdna_end": null,
"cdna_length": 2538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "c.1172C>T",
"hgvs_p": "p.Pro391Leu",
"transcript": "ENST00000513692.5",
"protein_id": "ENSP00000424235.1",
"transcript_support_level": 1,
"aa_start": 391,
"aa_end": null,
"aa_length": 519,
"cds_start": 1172,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 1447,
"cdna_end": null,
"cdna_length": 2391,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "n.*619C>T",
"hgvs_p": null,
"transcript": "ENST00000508261.5",
"protein_id": "ENSP00000422462.1",
"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": 1858,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "n.*619C>T",
"hgvs_p": null,
"transcript": "ENST00000508261.5",
"protein_id": "ENSP00000422462.1",
"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": 1858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "c.1250C>T",
"hgvs_p": "p.Pro417Leu",
"transcript": "NM_001278633.1",
"protein_id": "NP_001265562.1",
"transcript_support_level": null,
"aa_start": 417,
"aa_end": null,
"aa_length": 545,
"cds_start": 1250,
"cds_end": null,
"cds_length": 1638,
"cdna_start": 1468,
"cdna_end": null,
"cdna_length": 2398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "c.1250C>T",
"hgvs_p": "p.Pro417Leu",
"transcript": "NM_001278635.2",
"protein_id": "NP_001265564.1",
"transcript_support_level": null,
"aa_start": 417,
"aa_end": null,
"aa_length": 545,
"cds_start": 1250,
"cds_end": null,
"cds_length": 1638,
"cdna_start": 1434,
"cdna_end": null,
"cdna_length": 2378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "c.1250C>T",
"hgvs_p": "p.Pro417Leu",
"transcript": "ENST00000511126.2",
"protein_id": "ENSP00000421772.2",
"transcript_support_level": 3,
"aa_start": 417,
"aa_end": null,
"aa_length": 545,
"cds_start": 1250,
"cds_end": null,
"cds_length": 1638,
"cdna_start": 1468,
"cdna_end": null,
"cdna_length": 2398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "c.1172C>T",
"hgvs_p": "p.Pro391Leu",
"transcript": "NM_001278632.1",
"protein_id": "NP_001265561.1",
"transcript_support_level": null,
"aa_start": 391,
"aa_end": null,
"aa_length": 519,
"cds_start": 1172,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 1390,
"cdna_end": null,
"cdna_length": 2320,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "c.1172C>T",
"hgvs_p": "p.Pro391Leu",
"transcript": "NM_001278634.2",
"protein_id": "NP_001265563.1",
"transcript_support_level": null,
"aa_start": 391,
"aa_end": null,
"aa_length": 519,
"cds_start": 1172,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 1356,
"cdna_end": null,
"cdna_length": 2300,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "n.*553C>T",
"hgvs_p": null,
"transcript": "ENST00000717757.1",
"protein_id": "ENSP00000520645.1",
"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": 2234,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "n.1597C>T",
"hgvs_p": null,
"transcript": "ENST00000718124.1",
"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": 2541,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "n.*864C>T",
"hgvs_p": null,
"transcript": "ENST00000718125.1",
"protein_id": "ENSP00000520680.1",
"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": 2416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "c.*399C>T",
"hgvs_p": null,
"transcript": "ENST00000717758.1",
"protein_id": "ENSP00000520646.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 261,
"cds_start": -4,
"cds_end": null,
"cds_length": 786,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2404,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "n.*553C>T",
"hgvs_p": null,
"transcript": "ENST00000717757.1",
"protein_id": "ENSP00000520645.1",
"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": 2234,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"hgvs_c": "n.*864C>T",
"hgvs_p": null,
"transcript": "ENST00000718125.1",
"protein_id": "ENSP00000520680.1",
"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": 2416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IRX4",
"gene_hgnc_id": 6129,
"dbsnp": "rs1175075312",
"frequency_reference_population": 0.000013639304,
"hom_count_reference_population": 0,
"allele_count_reference_population": 21,
"gnomad_exomes_af": 0.0000144149,
"gnomad_genomes_af": 0.00000656953,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6928678750991821,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.559,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3466,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.278,
"phylop100way_prediction": "Uncertain_significance",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000231357.7",
"gene_symbol": "IRX4",
"hgnc_id": 6129,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1172C>T",
"hgvs_p": "p.Pro391Leu"
}
],
"clinvar_disease": "Tetralogy of Fallot",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Tetralogy of Fallot",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}