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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: 1-117934537-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=117934537&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "WDR3",
"hgnc_id": 12755,
"hgvs_c": "c.236A>G",
"hgvs_p": "p.His79Arg",
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_006784.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_score": 3,
"allele_count_reference_population": 40,
"alphamissense_prediction": "Uncertain_significance",
"alphamissense_score": 0.3856,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.06,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.7705143690109253,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 943,
"aa_ref": "H",
"aa_start": 79,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10004,
"cdna_start": 312,
"cds_end": null,
"cds_length": 2832,
"cds_start": 236,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_006784.3",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "c.236A>G",
"hgvs_p": "p.His79Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000349139.6",
"protein_coding": true,
"protein_id": "NP_006775.1",
"strand": true,
"transcript": "NM_006784.3",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 943,
"aa_ref": "H",
"aa_start": 79,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 10004,
"cdna_start": 312,
"cds_end": null,
"cds_length": 2832,
"cds_start": 236,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000349139.6",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "c.236A>G",
"hgvs_p": "p.His79Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006784.3",
"protein_coding": true,
"protein_id": "ENSP00000308179.4",
"strand": true,
"transcript": "ENST00000349139.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 40,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1035,
"cdna_start": null,
"cds_end": null,
"cds_length": 123,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000369441.7",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "c.*123A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000358449.3",
"strand": true,
"transcript": "ENST00000369441.7",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 943,
"aa_ref": "H",
"aa_start": 79,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4210,
"cdna_start": 1001,
"cds_end": null,
"cds_length": 2832,
"cds_start": 236,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000880604.1",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "c.236A>G",
"hgvs_p": "p.His79Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550663.1",
"strand": true,
"transcript": "ENST00000880604.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 943,
"aa_ref": "H",
"aa_start": 79,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3623,
"cdna_start": 414,
"cds_end": null,
"cds_length": 2832,
"cds_start": 236,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000880605.1",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "c.236A>G",
"hgvs_p": "p.His79Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550664.1",
"strand": true,
"transcript": "ENST00000880605.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 943,
"aa_ref": "H",
"aa_start": 79,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3693,
"cdna_start": 493,
"cds_end": null,
"cds_length": 2832,
"cds_start": 236,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000928994.1",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "c.236A>G",
"hgvs_p": "p.His79Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599053.1",
"strand": true,
"transcript": "ENST00000928994.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 943,
"aa_ref": "H",
"aa_start": 79,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4404,
"cdna_start": 373,
"cds_end": null,
"cds_length": 2832,
"cds_start": 236,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000947751.1",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "c.236A>G",
"hgvs_p": "p.His79Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617810.1",
"strand": true,
"transcript": "ENST00000947751.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 943,
"aa_ref": "H",
"aa_start": 79,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3547,
"cdna_start": 343,
"cds_end": null,
"cds_length": 2832,
"cds_start": 236,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000947753.1",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "c.236A>G",
"hgvs_p": "p.His79Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617812.1",
"strand": true,
"transcript": "ENST00000947753.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 943,
"aa_ref": "H",
"aa_start": 79,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3559,
"cdna_start": 356,
"cds_end": null,
"cds_length": 2832,
"cds_start": 236,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000947754.1",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "c.236A>G",
"hgvs_p": "p.His79Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617813.1",
"strand": true,
"transcript": "ENST00000947754.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 924,
"aa_ref": "H",
"aa_start": 79,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3444,
"cdna_start": 299,
"cds_end": null,
"cds_length": 2775,
"cds_start": 236,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000947752.1",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "c.236A>G",
"hgvs_p": "p.His79Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617811.1",
"strand": true,
"transcript": "ENST00000947752.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 732,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000471680.1",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "n.418A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000471680.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 680,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000487202.5",
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"hgvs_c": "n.337A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000487202.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs772788857",
"effect": "missense_variant",
"frequency_reference_population": 0.000024783363,
"gene_hgnc_id": 12755,
"gene_symbol": "WDR3",
"gnomad_exomes_ac": 38,
"gnomad_exomes_af": 0.0000259946,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131454,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.412,
"pos": 117934537,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.286,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07999999821186066,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.08,
"transcript": "NM_006784.3"
}
]
}