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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-10206756-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=10206756&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 10206756,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000380833.9",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN4",
"gene_hgnc_id": 2022,
"hgvs_c": "c.823G>A",
"hgvs_p": "p.Val275Met",
"transcript": "NM_001830.4",
"protein_id": "NP_001821.2",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 760,
"cds_start": 823,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 1223,
"cdna_end": null,
"cdna_length": 6759,
"mane_select": "ENST00000380833.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN4",
"gene_hgnc_id": 2022,
"hgvs_c": "c.823G>A",
"hgvs_p": "p.Val275Met",
"transcript": "ENST00000380833.9",
"protein_id": "ENSP00000370213.4",
"transcript_support_level": 1,
"aa_start": 275,
"aa_end": null,
"aa_length": 760,
"cds_start": 823,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 1223,
"cdna_end": null,
"cdna_length": 6759,
"mane_select": "NM_001830.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN4",
"gene_hgnc_id": 2022,
"hgvs_c": "c.847G>A",
"hgvs_p": "p.Val283Met",
"transcript": "ENST00000421085.7",
"protein_id": "ENSP00000405754.3",
"transcript_support_level": 5,
"aa_start": 283,
"aa_end": null,
"aa_length": 768,
"cds_start": 847,
"cds_end": null,
"cds_length": 2307,
"cdna_start": 932,
"cdna_end": null,
"cdna_length": 3581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN4",
"gene_hgnc_id": 2022,
"hgvs_c": "c.823G>A",
"hgvs_p": "p.Val275Met",
"transcript": "ENST00000380829.5",
"protein_id": "ENSP00000370209.1",
"transcript_support_level": 5,
"aa_start": 275,
"aa_end": null,
"aa_length": 729,
"cds_start": 823,
"cds_end": null,
"cds_length": 2190,
"cdna_start": 938,
"cdna_end": null,
"cdna_length": 2418,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN4",
"gene_hgnc_id": 2022,
"hgvs_c": "c.541G>A",
"hgvs_p": "p.Val181Met",
"transcript": "NM_001256944.2",
"protein_id": "NP_001243873.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 666,
"cds_start": 541,
"cds_end": null,
"cds_length": 2001,
"cdna_start": 968,
"cdna_end": null,
"cdna_length": 6504,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN4",
"gene_hgnc_id": 2022,
"hgvs_c": "c.541G>A",
"hgvs_p": "p.Val181Met",
"transcript": "ENST00000674669.1",
"protein_id": "ENSP00000501922.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 666,
"cds_start": 541,
"cds_end": null,
"cds_length": 2001,
"cdna_start": 631,
"cdna_end": null,
"cdna_length": 2227,
"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": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN4",
"gene_hgnc_id": 2022,
"hgvs_c": "n.*597G>A",
"hgvs_p": null,
"transcript": "ENST00000675144.1",
"protein_id": "ENSP00000501600.1",
"transcript_support_level": null,
"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": 3485,
"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": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN4",
"gene_hgnc_id": 2022,
"hgvs_c": "n.823G>A",
"hgvs_p": null,
"transcript": "ENST00000675769.1",
"protein_id": "ENSP00000502110.1",
"transcript_support_level": null,
"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": 3777,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN4",
"gene_hgnc_id": 2022,
"hgvs_c": "n.*597G>A",
"hgvs_p": null,
"transcript": "ENST00000675144.1",
"protein_id": "ENSP00000501600.1",
"transcript_support_level": null,
"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": 3485,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN4",
"gene_hgnc_id": 2022,
"hgvs_c": "c.*37G>A",
"hgvs_p": null,
"transcript": "ENST00000454850.1",
"protein_id": "ENSP00000403064.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 151,
"cds_start": -4,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 487,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CLCN4",
"gene_hgnc_id": 2022,
"dbsnp": "rs879255585",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8740160465240479,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.925,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9725,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.74,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.553,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000380833.9",
"gene_symbol": "CLCN4",
"hgnc_id": 2022,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.823G>A",
"hgvs_p": "p.Val275Met"
}
],
"clinvar_disease": "CLCN4-related disorder,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "CLCN4-related disorder|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}