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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: 9-36276927-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=36276927&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 36276927,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_001128227.3",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.18T>C",
"hgvs_p": "p.Tyr6Tyr",
"transcript": "NM_001128227.3",
"protein_id": "NP_001121699.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 753,
"cds_start": 18,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 52,
"cdna_end": null,
"cdna_length": 5220,
"mane_select": null,
"mane_plus": "ENST00000396594.8",
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.18T>C",
"hgvs_p": "p.Tyr6Tyr",
"transcript": "ENST00000396594.8",
"protein_id": "ENSP00000379839.3",
"transcript_support_level": 1,
"aa_start": 6,
"aa_end": null,
"aa_length": 753,
"cds_start": 18,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 52,
"cdna_end": null,
"cdna_length": 5220,
"mane_select": null,
"mane_plus": "NM_001128227.3",
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.-47T>C",
"hgvs_p": null,
"transcript": "ENST00000543356.7",
"protein_id": "ENSP00000437765.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 663,
"cds_start": -4,
"cds_end": null,
"cds_length": 1992,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.18T>C",
"hgvs_p": "p.Tyr6Tyr",
"transcript": "XM_005251334.5",
"protein_id": "XP_005251391.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 702,
"cds_start": 18,
"cds_end": null,
"cds_length": 2109,
"cdna_start": 52,
"cdna_end": null,
"cdna_length": 5067,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "n.50T>C",
"hgvs_p": null,
"transcript": "ENST00000644762.1",
"protein_id": null,
"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": 527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.-47T>C",
"hgvs_p": null,
"transcript": "NM_001190388.2",
"protein_id": "NP_001177317.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 663,
"cds_start": -4,
"cds_end": null,
"cds_length": 1992,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CLTA",
"gene_hgnc_id": 2090,
"hgvs_c": "n.*101+11353A>G",
"hgvs_p": null,
"transcript": "ENST00000464497.5",
"protein_id": "ENSP00000419158.1",
"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": 1890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124902150",
"gene_hgnc_id": null,
"hgvs_c": "n.297-7781A>G",
"hgvs_p": null,
"transcript": "XR_007061473.1",
"protein_id": null,
"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": 728,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"dbsnp": "rs200763627",
"frequency_reference_population": 6.8448986e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8449e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12438473105430603,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": 0.022,
"revel_prediction": "Benign",
"alphamissense_score": 0.5088,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.198,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001128227.3",
"gene_symbol": "GNE",
"hgnc_id": 23657,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.18T>C",
"hgvs_p": "p.Tyr6Tyr"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "XR_007061473.1",
"gene_symbol": "LOC124902150",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.297-7781A>G",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000464497.5",
"gene_symbol": "CLTA",
"hgnc_id": 2090,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "n.*101+11353A>G",
"hgvs_p": null
}
],
"clinvar_disease": "GNE myopathy,Sialuria",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "GNE myopathy;Sialuria",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}