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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: 5-138090621-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=138090621&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 138090621,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001300938.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT8A",
"gene_hgnc_id": 12788,
"hgvs_c": "c.658C>T",
"hgvs_p": "p.Arg220Trp",
"transcript": "NM_001300939.2",
"protein_id": "NP_001287868.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 369,
"cds_start": 658,
"cds_end": null,
"cds_length": 1110,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000506684.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001300939.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT8A",
"gene_hgnc_id": 12788,
"hgvs_c": "c.658C>T",
"hgvs_p": "p.Arg220Trp",
"transcript": "ENST00000506684.6",
"protein_id": "ENSP00000426653.1",
"transcript_support_level": 1,
"aa_start": 220,
"aa_end": null,
"aa_length": 369,
"cds_start": 658,
"cds_end": null,
"cds_length": 1110,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001300939.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000506684.6"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT8A",
"gene_hgnc_id": 12788,
"hgvs_c": "c.658C>T",
"hgvs_p": "p.Arg220Trp",
"transcript": "ENST00000504809.5",
"protein_id": "ENSP00000424809.1",
"transcript_support_level": 1,
"aa_start": 220,
"aa_end": null,
"aa_length": 359,
"cds_start": 658,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000504809.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT8A",
"gene_hgnc_id": 12788,
"hgvs_c": "c.604C>T",
"hgvs_p": "p.Arg202Trp",
"transcript": "ENST00000398754.1",
"protein_id": "ENSP00000381739.1",
"transcript_support_level": 1,
"aa_start": 202,
"aa_end": null,
"aa_length": 351,
"cds_start": 604,
"cds_end": null,
"cds_length": 1056,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000398754.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT8A",
"gene_hgnc_id": 12788,
"hgvs_c": "n.604C>T",
"hgvs_p": null,
"transcript": "ENST00000361560.6",
"protein_id": "ENSP00000354726.2",
"transcript_support_level": 1,
"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": "ENST00000361560.6"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT8A",
"gene_hgnc_id": 12788,
"hgvs_c": "c.658C>T",
"hgvs_p": "p.Arg220Trp",
"transcript": "NM_001300938.2",
"protein_id": "NP_001287867.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 386,
"cds_start": 658,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001300938.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT8A",
"gene_hgnc_id": 12788,
"hgvs_c": "c.604C>T",
"hgvs_p": "p.Arg202Trp",
"transcript": "NM_058244.4",
"protein_id": "NP_490645.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 351,
"cds_start": 604,
"cds_end": null,
"cds_length": 1056,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_058244.4"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT8A",
"gene_hgnc_id": 12788,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"transcript": "XM_017009826.2",
"protein_id": "XP_016865315.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 255,
"cds_start": 316,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009826.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "WNT8A",
"gene_hgnc_id": 12788,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"transcript": "XM_047417692.1",
"protein_id": "XP_047273648.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 255,
"cds_start": 316,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417692.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT8A",
"gene_hgnc_id": 12788,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"transcript": "XM_047417693.1",
"protein_id": "XP_047273649.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 255,
"cds_start": 316,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417693.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT8A",
"gene_hgnc_id": 12788,
"hgvs_c": "n.661C>T",
"hgvs_p": null,
"transcript": "NR_125351.2",
"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_125351.2"
}
],
"gene_symbol": "WNT8A",
"gene_hgnc_id": 12788,
"dbsnp": "rs749859751",
"frequency_reference_population": 0.000008673779,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000752452,
"gnomad_genomes_af": 0.0000197145,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9743150472640991,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.931,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4152,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.32,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.11,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,BS2",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 4,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001300938.2",
"gene_symbol": "WNT8A",
"hgnc_id": 12788,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.658C>T",
"hgvs_p": "p.Arg220Trp"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}