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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: 1-209790666-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=209790666&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 209790666,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000367021.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "c.889G>A",
"hgvs_p": "p.Val297Ile",
"transcript": "NM_006147.4",
"protein_id": "NP_006138.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 467,
"cds_start": 889,
"cds_end": null,
"cds_length": 1404,
"cdna_start": 1160,
"cdna_end": null,
"cdna_length": 4478,
"mane_select": "ENST00000367021.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "c.889G>A",
"hgvs_p": "p.Val297Ile",
"transcript": "ENST00000367021.8",
"protein_id": "ENSP00000355988.3",
"transcript_support_level": 1,
"aa_start": 297,
"aa_end": null,
"aa_length": 467,
"cds_start": 889,
"cds_end": null,
"cds_length": 1404,
"cdna_start": 1160,
"cdna_end": null,
"cdna_length": 4478,
"mane_select": "NM_006147.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289700",
"gene_hgnc_id": null,
"hgvs_c": "c.889G>A",
"hgvs_p": "p.Val297Ile",
"transcript": "ENST00000696133.1",
"protein_id": "ENSP00000512426.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 486,
"cds_start": 889,
"cds_end": null,
"cds_length": 1461,
"cdna_start": 1197,
"cdna_end": null,
"cdna_length": 5789,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "c.604G>A",
"hgvs_p": "p.Val202Ile",
"transcript": "NM_001206696.2",
"protein_id": "NP_001193625.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 372,
"cds_start": 604,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 911,
"cdna_end": null,
"cdna_length": 4229,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "c.604G>A",
"hgvs_p": "p.Val202Ile",
"transcript": "ENST00000542854.5",
"protein_id": "ENSP00000440532.1",
"transcript_support_level": 2,
"aa_start": 202,
"aa_end": null,
"aa_length": 372,
"cds_start": 604,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 944,
"cdna_end": null,
"cdna_length": 4256,
"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": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "n.*399G>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": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "n.*316G>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": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "n.*399G>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": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "n.*316G>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": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "c.*60G>A",
"hgvs_p": null,
"transcript": "ENST00000456314.1",
"protein_id": "ENSP00000403855.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 275,
"cds_start": -4,
"cds_end": null,
"cds_length": 829,
"cdna_start": null,
"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": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"hgvs_c": "n.*72G>A",
"hgvs_p": null,
"transcript": "ENST00000464698.1",
"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": 596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IRF6",
"gene_hgnc_id": 6121,
"dbsnp": "rs779827384",
"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": 0.8719597458839417,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.583,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.313,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.391,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000367021.8",
"gene_symbol": "IRF6",
"hgnc_id": 6121,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.889G>A",
"hgvs_p": "p.Val297Ile"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM1",
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000696133.1",
"gene_symbol": "ENSG00000289700",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.889G>A",
"hgvs_p": "p.Val297Ile"
}
],
"clinvar_disease": " susceptibility to,Orofacial cleft 6,Popliteal pterygium syndrome,Van der Woude syndrome",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Orofacial cleft 6, susceptibility to;Popliteal pterygium syndrome;Van der Woude syndrome",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}