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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: X-106901485-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=106901485&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 106901485,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_138382.3",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIPPLY1",
"gene_hgnc_id": 25117,
"hgvs_c": "c.285T>A",
"hgvs_p": "p.His95Gln",
"transcript": "NM_138382.3",
"protein_id": "NP_612391.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 151,
"cds_start": 285,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000276173.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_138382.3"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIPPLY1",
"gene_hgnc_id": 25117,
"hgvs_c": "c.285T>A",
"hgvs_p": "p.His95Gln",
"transcript": "ENST00000276173.5",
"protein_id": "ENSP00000276173.4",
"transcript_support_level": 1,
"aa_start": 95,
"aa_end": null,
"aa_length": 151,
"cds_start": 285,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_138382.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000276173.5"
},
{
"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": "CLDN2",
"gene_hgnc_id": 2041,
"hgvs_c": "c.-179+981A>T",
"hgvs_p": null,
"transcript": "ENST00000541806.6",
"protein_id": "ENSP00000441283.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 230,
"cds_start": null,
"cds_end": null,
"cds_length": 693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000541806.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RIPPLY1",
"gene_hgnc_id": 25117,
"hgvs_c": "c.156-577T>A",
"hgvs_p": null,
"transcript": "ENST00000411805.1",
"protein_id": "ENSP00000400539.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 104,
"cds_start": null,
"cds_end": null,
"cds_length": 315,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000411805.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CLDN2",
"gene_hgnc_id": 2041,
"hgvs_c": "c.-179+981A>T",
"hgvs_p": null,
"transcript": "NM_001171092.1",
"protein_id": "NP_001164563.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 230,
"cds_start": null,
"cds_end": null,
"cds_length": 693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001171092.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CLDN2",
"gene_hgnc_id": 2041,
"hgvs_c": "c.-179+1281A>T",
"hgvs_p": null,
"transcript": "ENST00000899662.1",
"protein_id": "ENSP00000569721.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 230,
"cds_start": null,
"cds_end": null,
"cds_length": 693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899662.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RIPPLY1",
"gene_hgnc_id": 25117,
"hgvs_c": "c.156-577T>A",
"hgvs_p": null,
"transcript": "NM_001171706.2",
"protein_id": "NP_001165177.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 104,
"cds_start": null,
"cds_end": null,
"cds_length": 315,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001171706.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MORC4",
"gene_hgnc_id": 23485,
"hgvs_c": "c.111-85699T>A",
"hgvs_p": null,
"transcript": "ENST00000604604.1",
"protein_id": "ENSP00000474750.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 37,
"cds_start": null,
"cds_end": null,
"cds_length": 114,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000604604.1"
}
],
"gene_symbol": "RIPPLY1",
"gene_hgnc_id": 25117,
"dbsnp": "rs200487665",
"frequency_reference_population": 0.0000016534268,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 9.11138e-7,
"gnomad_genomes_af": 0.0000089222,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1132664680480957,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.163,
"revel_prediction": "Benign",
"alphamissense_score": 0.1654,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.274,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_138382.3",
"gene_symbol": "RIPPLY1",
"hgnc_id": 25117,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.285T>A",
"hgvs_p": "p.His95Gln"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001171092.1",
"gene_symbol": "CLDN2",
"hgnc_id": 2041,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.-179+981A>T",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000604604.1",
"gene_symbol": "MORC4",
"hgnc_id": 23485,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.111-85699T>A",
"hgvs_p": null
}
],
"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
}