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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: 1-209796463-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=209796463&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 209796463,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000367021.8",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "c.264T>A",
"hgvs_p": "p.Asn88Lys",
"transcript": "NM_006147.4",
"protein_id": "NP_006138.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 467,
"cds_start": 264,
"cds_end": null,
"cds_length": 1404,
"cdna_start": 535,
"cdna_end": null,
"cdna_length": 4478,
"mane_select": "ENST00000367021.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "c.264T>A",
"hgvs_p": "p.Asn88Lys",
"transcript": "ENST00000367021.8",
"protein_id": "ENSP00000355988.3",
"transcript_support_level": 1,
"aa_start": 88,
"aa_end": null,
"aa_length": 467,
"cds_start": 264,
"cds_end": null,
"cds_length": 1404,
"cdna_start": 535,
"cdna_end": null,
"cdna_length": 4478,
"mane_select": "NM_006147.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289700",
"gene_hgnc_id": null,
"hgvs_c": "c.264T>A",
"hgvs_p": "p.Asn88Lys",
"transcript": "ENST00000696133.1",
"protein_id": "ENSP00000512426.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 486,
"cds_start": 264,
"cds_end": null,
"cds_length": 1461,
"cdna_start": 572,
"cdna_end": null,
"cdna_length": 5789,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "c.264T>A",
"hgvs_p": "p.Asn88Lys",
"transcript": "ENST00000456314.1",
"protein_id": "ENSP00000403855.1",
"transcript_support_level": 3,
"aa_start": 88,
"aa_end": null,
"aa_length": 275,
"cds_start": 264,
"cds_end": null,
"cds_length": 829,
"cdna_start": 462,
"cdna_end": null,
"cdna_length": 1027,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "n.264T>A",
"hgvs_p": null,
"transcript": "ENST00000643798.1",
"protein_id": "ENSP00000496669.1",
"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": 1697,
"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": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "n.264T>A",
"hgvs_p": null,
"transcript": "ENST00000696134.1",
"protein_id": "ENSP00000512427.1",
"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": 4558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "c.-22T>A",
"hgvs_p": null,
"transcript": "NM_001206696.2",
"protein_id": "NP_001193625.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 372,
"cds_start": -4,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4229,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "c.-22T>A",
"hgvs_p": null,
"transcript": "ENST00000542854.5",
"protein_id": "ENSP00000440532.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 372,
"cds_start": -4,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4256,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"dbsnp": "rs1553248265",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9885913133621216,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.864,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.999,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.809,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Strong",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000367021.8",
"gene_symbol": "IRF6",
"hgnc_id": 6121,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.264T>A",
"hgvs_p": "p.Asn88Lys"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000696133.1",
"gene_symbol": "ENSG00000289700",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.264T>A",
"hgvs_p": "p.Asn88Lys"
}
],
"clinvar_disease": " susceptibility to,Orofacial cleft 6,Popliteal pterygium syndrome,Van der Woude syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Orofacial cleft 6, susceptibility to;Popliteal pterygium syndrome;Van der Woude syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}