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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-129569399-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=129569399&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 129569399,
"ref": "G",
"alt": "T",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "ENST00000371113.9",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "c.1602G>T",
"hgvs_p": "p.Gly534Gly",
"transcript": "NM_000276.4",
"protein_id": "NP_000267.2",
"transcript_support_level": null,
"aa_start": 534,
"aa_end": null,
"aa_length": 901,
"cds_start": 1602,
"cds_end": null,
"cds_length": 2706,
"cdna_start": 1783,
"cdna_end": null,
"cdna_length": 5173,
"mane_select": "ENST00000371113.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "c.1602G>T",
"hgvs_p": "p.Gly534Gly",
"transcript": "ENST00000371113.9",
"protein_id": "ENSP00000360154.4",
"transcript_support_level": 1,
"aa_start": 534,
"aa_end": null,
"aa_length": 901,
"cds_start": 1602,
"cds_end": null,
"cds_length": 2706,
"cdna_start": 1783,
"cdna_end": null,
"cdna_length": 5173,
"mane_select": "NM_000276.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "c.1602G>T",
"hgvs_p": "p.Gly534Gly",
"transcript": "ENST00000357121.5",
"protein_id": "ENSP00000349635.5",
"transcript_support_level": 1,
"aa_start": 534,
"aa_end": null,
"aa_length": 893,
"cds_start": 1602,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 1767,
"cdna_end": null,
"cdna_length": 5138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "c.1605G>T",
"hgvs_p": "p.Gly535Gly",
"transcript": "NM_001318784.2",
"protein_id": "NP_001305713.1",
"transcript_support_level": null,
"aa_start": 535,
"aa_end": null,
"aa_length": 902,
"cds_start": 1605,
"cds_end": null,
"cds_length": 2709,
"cdna_start": 1786,
"cdna_end": null,
"cdna_length": 5176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "c.1602G>T",
"hgvs_p": "p.Gly534Gly",
"transcript": "NM_001587.4",
"protein_id": "NP_001578.2",
"transcript_support_level": null,
"aa_start": 534,
"aa_end": null,
"aa_length": 893,
"cds_start": 1602,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 1783,
"cdna_end": null,
"cdna_length": 5149,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "n.*1441G>T",
"hgvs_p": null,
"transcript": "ENST00000646010.1",
"protein_id": "ENSP00000494940.1",
"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": 5021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "n.711G>T",
"hgvs_p": null,
"transcript": "ENST00000646914.1",
"protein_id": "ENSP00000493809.1",
"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": 4079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "n.1251G>T",
"hgvs_p": null,
"transcript": "ENST00000647245.1",
"protein_id": "ENSP00000495615.1",
"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": 4325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "n.*1894G>T",
"hgvs_p": null,
"transcript": "ENST00000691455.1",
"protein_id": "ENSP00000510265.1",
"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": 2898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "n.*1510G>T",
"hgvs_p": null,
"transcript": "ENST00000693473.1",
"protein_id": "ENSP00000509548.1",
"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": 5090,
"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": 16,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "n.*1441G>T",
"hgvs_p": null,
"transcript": "ENST00000646010.1",
"protein_id": "ENSP00000494940.1",
"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": 5021,
"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": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "n.*1894G>T",
"hgvs_p": null,
"transcript": "ENST00000691455.1",
"protein_id": "ENSP00000510265.1",
"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": 2898,
"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": 17,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"hgvs_c": "n.*1510G>T",
"hgvs_p": null,
"transcript": "ENST00000693473.1",
"protein_id": "ENSP00000509548.1",
"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": 5090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OCRL",
"gene_hgnc_id": 8108,
"dbsnp": "rs773214157",
"frequency_reference_population": 9.1295186e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 9.12952e-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": -0.23000000417232513,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9620000123977661,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.588,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.37,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.999981033003531,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000371113.9",
"gene_symbol": "OCRL",
"hgnc_id": 8108,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1602G>T",
"hgvs_p": "p.Gly534Gly"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}