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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-129562396-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=129562396&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "OCRL",
"hgnc_id": 8108,
"hgvs_c": "c.955C>T",
"hgvs_p": "p.Arg319Cys",
"inheritance_mode": "XL",
"pathogenic_score": 20,
"score": 20,
"transcript": "NM_001318784.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_score": 20,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.8417,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.73,
"chr": "X",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Dent disease type 2,Lowe syndrome,OCRL-related disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1 O:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9893170595169067,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 901,
"aa_ref": "R",
"aa_start": 318,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5173,
"cdna_start": 1133,
"cds_end": null,
"cds_length": 2706,
"cds_start": 952,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_000276.4",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.952C>T",
"hgvs_p": "p.Arg318Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000371113.9",
"protein_coding": true,
"protein_id": "NP_000267.2",
"strand": true,
"transcript": "NM_000276.4",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 901,
"aa_ref": "R",
"aa_start": 318,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5173,
"cdna_start": 1133,
"cds_end": null,
"cds_length": 2706,
"cds_start": 952,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000371113.9",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.952C>T",
"hgvs_p": "p.Arg318Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000276.4",
"protein_coding": true,
"protein_id": "ENSP00000360154.4",
"strand": true,
"transcript": "ENST00000371113.9",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 893,
"aa_ref": "R",
"aa_start": 318,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5138,
"cdna_start": 1117,
"cds_end": null,
"cds_length": 2682,
"cds_start": 952,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000357121.5",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.952C>T",
"hgvs_p": "p.Arg318Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000349635.5",
"strand": true,
"transcript": "ENST00000357121.5",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 902,
"aa_ref": "R",
"aa_start": 319,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5176,
"cdna_start": 1136,
"cds_end": null,
"cds_length": 2709,
"cds_start": 955,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001318784.2",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.955C>T",
"hgvs_p": "p.Arg319Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305713.1",
"strand": true,
"transcript": "NM_001318784.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 900,
"aa_ref": "R",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5180,
"cdna_start": 1148,
"cds_end": null,
"cds_length": 2703,
"cds_start": 949,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000949289.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Arg317Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619348.1",
"strand": true,
"transcript": "ENST00000949289.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 898,
"aa_ref": "R",
"aa_start": 315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5196,
"cdna_start": 1156,
"cds_end": null,
"cds_length": 2697,
"cds_start": 943,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000927771.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.943C>T",
"hgvs_p": "p.Arg315Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000597830.1",
"strand": true,
"transcript": "ENST00000927771.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 893,
"aa_ref": "R",
"aa_start": 318,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5149,
"cdna_start": 1133,
"cds_end": null,
"cds_length": 2682,
"cds_start": 952,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001587.4",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.952C>T",
"hgvs_p": "p.Arg318Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001578.2",
"strand": true,
"transcript": "NM_001587.4",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 892,
"aa_ref": "R",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5099,
"cdna_start": 1088,
"cds_end": null,
"cds_length": 2679,
"cds_start": 949,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000949290.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Arg317Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619349.1",
"strand": true,
"transcript": "ENST00000949290.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 892,
"aa_ref": "R",
"aa_start": 318,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5030,
"cdna_start": 1023,
"cds_end": null,
"cds_length": 2679,
"cds_start": 952,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000949291.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.952C>T",
"hgvs_p": "p.Arg318Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619350.1",
"strand": true,
"transcript": "ENST00000949291.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 890,
"aa_ref": "R",
"aa_start": 315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5197,
"cdna_start": 1181,
"cds_end": null,
"cds_length": 2673,
"cds_start": 943,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000851833.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.943C>T",
"hgvs_p": "p.Arg315Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521892.1",
"strand": true,
"transcript": "ENST00000851833.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 871,
"aa_ref": "R",
"aa_start": 288,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5129,
"cdna_start": 1089,
"cds_end": null,
"cds_length": 2616,
"cds_start": 862,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000927770.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.862C>T",
"hgvs_p": "p.Arg288Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000597829.1",
"strand": true,
"transcript": "ENST00000927770.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 863,
"aa_ref": "R",
"aa_start": 288,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5112,
"cdna_start": 1096,
"cds_end": null,
"cds_length": 2592,
"cds_start": 862,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000851834.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "c.862C>T",
"hgvs_p": "p.Arg288Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521893.1",
"strand": true,
"transcript": "ENST00000851834.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5021,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 25,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000646010.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "n.*791C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000494940.1",
"strand": true,
"transcript": "ENST00000646010.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4079,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000646914.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "n.61C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000493809.1",
"strand": true,
"transcript": "ENST00000646914.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4325,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000647245.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "n.601C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000495615.1",
"strand": true,
"transcript": "ENST00000647245.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2898,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000691455.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "n.*1244C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000510265.1",
"strand": true,
"transcript": "ENST00000691455.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5090,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 26,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000693473.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "n.*860C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000509548.1",
"strand": true,
"transcript": "ENST00000693473.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5021,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 25,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000646010.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "n.*791C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000494940.1",
"strand": true,
"transcript": "ENST00000646010.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2898,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000691455.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "n.*1244C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000510265.1",
"strand": true,
"transcript": "ENST00000691455.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5090,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 26,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000693473.1",
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"hgvs_c": "n.*860C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000509548.1",
"strand": true,
"transcript": "ENST00000693473.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs137853263",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 8108,
"gene_symbol": "OCRL",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Dent disease type 2|Lowe syndrome|not provided|OCRL-related disorder",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.556,
"pos": 129562396,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.986,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07999999821186066,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.08,
"transcript": "NM_001318784.2"
}
]
}