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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: 15-62028419-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=62028419&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 62028419,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_020821.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 85,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.387C>T",
"hgvs_p": "p.Gly129Gly",
"transcript": "NM_020821.3",
"protein_id": "NP_065872.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 3753,
"cds_start": 387,
"cds_end": null,
"cds_length": 11262,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000644861.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020821.3"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 85,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.387C>T",
"hgvs_p": "p.Gly129Gly",
"transcript": "ENST00000644861.2",
"protein_id": "ENSP00000493560.2",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 3753,
"cds_start": 387,
"cds_end": null,
"cds_length": 11262,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020821.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644861.2"
},
{
"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": 83,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.386-4899C>T",
"hgvs_p": null,
"transcript": "ENST00000249837.7",
"protein_id": "ENSP00000249837.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 3710,
"cds_start": null,
"cds_end": null,
"cds_length": 11133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000249837.7"
},
{
"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": 80,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.386-4899C>T",
"hgvs_p": null,
"transcript": "ENST00000395898.3",
"protein_id": "ENSP00000379235.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 3585,
"cds_start": null,
"cds_end": null,
"cds_length": 10758,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395898.3"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 82,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.387C>T",
"hgvs_p": "p.Gly129Gly",
"transcript": "NM_001018088.3",
"protein_id": "NP_001018098.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 3628,
"cds_start": 387,
"cds_end": null,
"cds_length": 10887,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001018088.3"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 82,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.387C>T",
"hgvs_p": "p.Gly129Gly",
"transcript": "ENST00000645819.1",
"protein_id": "ENSP00000496179.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 3628,
"cds_start": 387,
"cds_end": null,
"cds_length": 10887,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000645819.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.387C>T",
"hgvs_p": "p.Gly129Gly",
"transcript": "XM_011521713.4",
"protein_id": "XP_011520015.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 3059,
"cds_start": 387,
"cds_end": null,
"cds_length": 9180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011521713.4"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.387C>T",
"hgvs_p": "p.Gly129Gly",
"transcript": "XM_047432741.1",
"protein_id": "XP_047288697.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 3059,
"cds_start": 387,
"cds_end": null,
"cds_length": 9180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047432741.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.387C>T",
"hgvs_p": "p.Gly129Gly",
"transcript": "XM_011521714.3",
"protein_id": "XP_011520016.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 2566,
"cds_start": 387,
"cds_end": null,
"cds_length": 7701,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011521714.3"
},
{
"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": 83,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.386-4899C>T",
"hgvs_p": null,
"transcript": "NM_017684.5",
"protein_id": "NP_060154.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3710,
"cds_start": null,
"cds_end": null,
"cds_length": 11133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017684.5"
},
{
"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": 80,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.386-4899C>T",
"hgvs_p": null,
"transcript": "NM_018080.4",
"protein_id": "NP_060550.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3585,
"cds_start": null,
"cds_end": null,
"cds_length": 10758,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018080.4"
},
{
"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": 57,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "c.386-4899C>T",
"hgvs_p": null,
"transcript": "XM_047432742.1",
"protein_id": "XP_047288698.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2523,
"cds_start": null,
"cds_end": null,
"cds_length": 7572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047432742.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 83,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"hgvs_c": "n.460C>T",
"hgvs_p": null,
"transcript": "XR_007064464.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007064464.1"
}
],
"gene_symbol": "VPS13C",
"gene_hgnc_id": 23594,
"dbsnp": "rs139665824",
"frequency_reference_population": 0.0004780838,
"hom_count_reference_population": 1,
"allele_count_reference_population": 771,
"gnomad_exomes_af": 0.000469649,
"gnomad_genomes_af": 0.000559122,
"gnomad_exomes_ac": 686,
"gnomad_genomes_ac": 85,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3499999940395355,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.03799999877810478,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.612,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000202697415200716,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7,BS1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_020821.3",
"gene_symbol": "VPS13C",
"hgnc_id": 23594,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.387C>T",
"hgvs_p": "p.Gly129Gly"
}
],
"clinvar_disease": "Autosomal recessive early-onset Parkinson disease 23,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "Autosomal recessive early-onset Parkinson disease 23|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}