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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: 2-218890289-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=218890289&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 218890289,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_025216.3",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.682T>A",
"hgvs_p": "p.Phe228Ile",
"transcript": "NM_025216.3",
"protein_id": "NP_079492.2",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 417,
"cds_start": 682,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000258411.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_025216.3"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.682T>A",
"hgvs_p": "p.Phe228Ile",
"transcript": "ENST00000258411.8",
"protein_id": "ENSP00000258411.3",
"transcript_support_level": 1,
"aa_start": 228,
"aa_end": null,
"aa_length": 417,
"cds_start": 682,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_025216.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000258411.8"
},
{
"aa_ref": "F",
"aa_alt": "I",
"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": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.997T>A",
"hgvs_p": "p.Phe333Ile",
"transcript": "ENST00000964557.1",
"protein_id": "ENSP00000634616.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 522,
"cds_start": 997,
"cds_end": null,
"cds_length": 1569,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964557.1"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.712T>A",
"hgvs_p": "p.Phe238Ile",
"transcript": "ENST00000865256.1",
"protein_id": "ENSP00000535315.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 427,
"cds_start": 712,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865256.1"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.586T>A",
"hgvs_p": "p.Phe196Ile",
"transcript": "XM_011511929.3",
"protein_id": "XP_011510231.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 385,
"cds_start": 586,
"cds_end": null,
"cds_length": 1158,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011511929.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.263-2485T>A",
"hgvs_p": null,
"transcript": "ENST00000458582.1",
"protein_id": "ENSP00000388812.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 210,
"cds_start": null,
"cds_end": null,
"cds_length": 635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000458582.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.377-2485T>A",
"hgvs_p": null,
"transcript": "XM_011511930.2",
"protein_id": "XP_011510232.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": null,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011511930.2"
},
{
"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": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "n.*190T>A",
"hgvs_p": null,
"transcript": "ENST00000483911.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000483911.1"
}
],
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"dbsnp": "rs121908120",
"frequency_reference_population": 0.020787625,
"hom_count_reference_population": 449,
"allele_count_reference_population": 33427,
"gnomad_exomes_af": 0.0214924,
"gnomad_genomes_af": 0.0140464,
"gnomad_exomes_ac": 31289,
"gnomad_genomes_ac": 2138,
"gnomad_exomes_homalt": 427,
"gnomad_genomes_homalt": 22,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.013546854257583618,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.863,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9532,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.937,
"phylop100way_prediction": "Pathogenic",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PS3,PM1,PP3,PP5,BP4",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 1,
"pathogenic_score": 8,
"criteria": [
"PS3",
"PM1",
"PP3",
"PP5",
"BP4"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_025216.3",
"gene_symbol": "WNT10A",
"hgnc_id": 13829,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,SD,AD",
"hgvs_c": "c.682T>A",
"hgvs_p": "p.Phe228Ile"
}
],
"clinvar_disease": " 4, selective,Ectodermal dysplasia,Ectodermal dysplasia WNT10A related,Hypohidrotic ectodermal dysplasia,Inborn genetic diseases,Odonto-onycho-dermal dysplasia,Schöpf-Schulz-Passarge syndrome,See cases,Tooth agenesis,WNT10A-related disorder,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:20 LP:4 US:1 O:3",
"phenotype_combined": "Odonto-onycho-dermal dysplasia|Tooth agenesis, selective, 4|Tooth agenesis|not provided|Ectodermal dysplasia|Tooth agenesis, selective, 4;Odonto-onycho-dermal dysplasia|Tooth agenesis, selective, 4;Odonto-onycho-dermal dysplasia;Schöpf-Schulz-Passarge syndrome|Inborn genetic diseases|Tooth agenesis, selective, 4;Schöpf-Schulz-Passarge syndrome|Hypohidrotic ectodermal dysplasia|Ectodermal dysplasia WNT10A related|WNT10A-related disorder|See cases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}