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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: 18-32018944-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=32018944&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 32018944,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000217740.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF125",
"gene_hgnc_id": 21150,
"hgvs_c": "c.81C>A",
"hgvs_p": "p.Asp27Glu",
"transcript": "NM_017831.4",
"protein_id": "NP_060301.2",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 232,
"cds_start": 81,
"cds_end": null,
"cds_length": 699,
"cdna_start": 120,
"cdna_end": null,
"cdna_length": 5573,
"mane_select": "ENST00000217740.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF125",
"gene_hgnc_id": 21150,
"hgvs_c": "c.81C>A",
"hgvs_p": "p.Asp27Glu",
"transcript": "ENST00000217740.4",
"protein_id": "ENSP00000217740.3",
"transcript_support_level": 1,
"aa_start": 27,
"aa_end": null,
"aa_length": 232,
"cds_start": 81,
"cds_end": null,
"cds_length": 699,
"cdna_start": 120,
"cdna_end": null,
"cdna_length": 5573,
"mane_select": "NM_017831.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF125",
"gene_hgnc_id": 21150,
"hgvs_c": "c.81C>A",
"hgvs_p": "p.Asp27Glu",
"transcript": "NM_001436860.1",
"protein_id": "NP_001423789.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 227,
"cds_start": 81,
"cds_end": null,
"cds_length": 684,
"cdna_start": 120,
"cdna_end": null,
"cdna_length": 3560,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF125",
"gene_hgnc_id": 21150,
"hgvs_c": "c.81C>A",
"hgvs_p": "p.Asp27Glu",
"transcript": "ENST00000718283.1",
"protein_id": "ENSP00000520722.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 227,
"cds_start": 81,
"cds_end": null,
"cds_length": 684,
"cdna_start": 120,
"cdna_end": null,
"cdna_length": 898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF125",
"gene_hgnc_id": 21150,
"hgvs_c": "c.81C>A",
"hgvs_p": "p.Asp27Glu",
"transcript": "NM_001436861.1",
"protein_id": "NP_001423790.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 191,
"cds_start": 81,
"cds_end": null,
"cds_length": 576,
"cdna_start": 120,
"cdna_end": null,
"cdna_length": 3452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF125",
"gene_hgnc_id": 21150,
"hgvs_c": "c.81C>A",
"hgvs_p": "p.Asp27Glu",
"transcript": "ENST00000718284.1",
"protein_id": "ENSP00000520723.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 191,
"cds_start": 81,
"cds_end": null,
"cds_length": 576,
"cdna_start": 120,
"cdna_end": null,
"cdna_length": 790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF125",
"gene_hgnc_id": 21150,
"hgvs_c": "c.81C>A",
"hgvs_p": "p.Asp27Glu",
"transcript": "XM_011526046.4",
"protein_id": "XP_011524348.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 196,
"cds_start": 81,
"cds_end": null,
"cds_length": 591,
"cdna_start": 120,
"cdna_end": null,
"cdna_length": 5465,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF125",
"gene_hgnc_id": 21150,
"hgvs_c": "c.81C>A",
"hgvs_p": "p.Asp27Glu",
"transcript": "XM_047437561.1",
"protein_id": "XP_047293517.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 139,
"cds_start": 81,
"cds_end": null,
"cds_length": 420,
"cdna_start": 120,
"cdna_end": null,
"cdna_length": 608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000263917",
"gene_hgnc_id": null,
"hgvs_c": "n.116C>A",
"hgvs_p": null,
"transcript": "ENST00000583184.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RNF125",
"gene_hgnc_id": 21150,
"dbsnp": "rs776932441",
"frequency_reference_population": 0.000060740163,
"hom_count_reference_population": 0,
"allele_count_reference_population": 98,
"gnomad_exomes_af": 0.0000636468,
"gnomad_genomes_af": 0.0000328429,
"gnomad_exomes_ac": 93,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.054367393255233765,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.109,
"revel_prediction": "Benign",
"alphamissense_score": 0.0805,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.01,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000217740.4",
"gene_symbol": "RNF125",
"hgnc_id": 21150,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.81C>A",
"hgvs_p": "p.Asp27Glu"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000583184.1",
"gene_symbol": "ENSG00000263917",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.116C>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Tenorio syndrome,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Tenorio syndrome|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}