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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: 2-108929288-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=108929288&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 108929288,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000258443.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EDAR",
"gene_hgnc_id": 2895,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Arg89His",
"transcript": "NM_022336.4",
"protein_id": "NP_071731.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 448,
"cds_start": 266,
"cds_end": null,
"cds_length": 1347,
"cdna_start": 545,
"cdna_end": null,
"cdna_length": 4062,
"mane_select": "ENST00000258443.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EDAR",
"gene_hgnc_id": 2895,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Arg89His",
"transcript": "ENST00000258443.7",
"protein_id": "ENSP00000258443.2",
"transcript_support_level": 1,
"aa_start": 89,
"aa_end": null,
"aa_length": 448,
"cds_start": 266,
"cds_end": null,
"cds_length": 1347,
"cdna_start": 545,
"cdna_end": null,
"cdna_length": 4062,
"mane_select": "NM_022336.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EDAR",
"gene_hgnc_id": 2895,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Arg89His",
"transcript": "ENST00000376651.1",
"protein_id": "ENSP00000365839.1",
"transcript_support_level": 2,
"aa_start": 89,
"aa_end": null,
"aa_length": 480,
"cds_start": 266,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 697,
"cdna_end": null,
"cdna_length": 4303,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EDAR",
"gene_hgnc_id": 2895,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Arg89His",
"transcript": "ENST00000409271.5",
"protein_id": "ENSP00000386371.1",
"transcript_support_level": 2,
"aa_start": 89,
"aa_end": null,
"aa_length": 480,
"cds_start": 266,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 710,
"cdna_end": null,
"cdna_length": 4323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EDAR",
"gene_hgnc_id": 2895,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Arg89His",
"transcript": "XM_006712204.2",
"protein_id": "XP_006712267.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 480,
"cds_start": 266,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 545,
"cdna_end": null,
"cdna_length": 4158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 25,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "RANBP2",
"gene_hgnc_id": 9848,
"hgvs_c": "c.8370+156242C>T",
"hgvs_p": null,
"transcript": "XM_047445367.1",
"protein_id": "XP_047301323.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2807,
"cds_start": -4,
"cds_end": null,
"cds_length": 8424,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9393,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EDAR",
"gene_hgnc_id": 2895,
"dbsnp": "rs121908450",
"frequency_reference_population": 0.000016108208,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000164175,
"gnomad_genomes_af": 0.0000131384,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.967461109161377,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.799,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7501,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.36,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.478,
"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": 17,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM5,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 17,
"benign_score": 0,
"pathogenic_score": 17,
"criteria": [
"PM1",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000258443.7",
"gene_symbol": "EDAR",
"hgnc_id": 2895,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Arg89His"
},
{
"score": 8,
"benign_score": 4,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong",
"BS2"
],
"verdict": "Likely_pathogenic",
"transcript": "XM_047445367.1",
"gene_symbol": "RANBP2",
"hgnc_id": 9848,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.8370+156242C>T",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal dominant, autosomal recessive, hypohidrotic/hair/nail type, hypohidrotic/hair/tooth type,Autosomal recessive hypohidrotic ectodermal dysplasia syndrome,Ectodermal dysplasia 10A,Ectodermal dysplasia 10B,Ectodermal dysplasia 10a,Mitochondrial DNA depletion syndrome 4b,Progressive sclerosing poliodystrophy",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Ectodermal dysplasia 10B, hypohidrotic/hair/tooth type, autosomal recessive|Ectodermal dysplasia 10a, hypohidrotic/hair/tooth type, autosomal dominant|Mitochondrial DNA depletion syndrome 4b;Progressive sclerosing poliodystrophy|Ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant|Autosomal recessive hypohidrotic ectodermal dysplasia syndrome;Ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}