← Back to variant description
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-41151058-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=41151058&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 41151058,
"ref": "G",
"alt": "A",
"effect": "splice_donor_variant,intron_variant",
"transcript": "ENST00000378308.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "NM_001039591.3",
"protein_id": "NP_001034680.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2554,
"cds_start": -4,
"cds_end": null,
"cds_length": 7665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12543,
"mane_select": "ENST00000378308.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "ENST00000378308.7",
"protein_id": "ENSP00000367558.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2554,
"cds_start": -4,
"cds_end": null,
"cds_length": 7665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12543,
"mane_select": "NM_001039591.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "NM_001410748.1",
"protein_id": "NP_001397677.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2575,
"cds_start": -4,
"cds_end": null,
"cds_length": 7728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "ENST00000703987.1",
"protein_id": "ENSP00000515604.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2575,
"cds_start": -4,
"cds_end": null,
"cds_length": 7728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "NM_001039590.3",
"protein_id": "NP_001034679.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2570,
"cds_start": -4,
"cds_end": null,
"cds_length": 7713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "ENST00000324545.9",
"protein_id": "ENSP00000316357.6",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2570,
"cds_start": -4,
"cds_end": null,
"cds_length": 7713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "NM_001410749.1",
"protein_id": "NP_001397678.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2559,
"cds_start": -4,
"cds_end": null,
"cds_length": 7680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "NM_001437534.1",
"protein_id": "NP_001424463.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2559,
"cds_start": -4,
"cds_end": null,
"cds_length": 7680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "ENST00000703986.1",
"protein_id": "ENSP00000515603.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2559,
"cds_start": -4,
"cds_end": null,
"cds_length": 7680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12490,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "ENST00000704650.1",
"protein_id": "ENSP00000515975.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2554,
"cds_start": -4,
"cds_end": null,
"cds_length": 7665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9555,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1610+1G>A",
"hgvs_p": null,
"transcript": "ENST00000704651.1",
"protein_id": "ENSP00000515976.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2503,
"cds_start": -4,
"cds_end": null,
"cds_length": 7512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9282,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "ENST00000704649.1",
"protein_id": "ENSP00000515974.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1273,
"cds_start": -4,
"cds_end": null,
"cds_length": 3822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8700,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "n.992+1G>A",
"hgvs_p": null,
"transcript": "ENST00000704652.1",
"protein_id": "ENSP00000515977.1",
"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": 10819,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "n.244-1890G>A",
"hgvs_p": null,
"transcript": "ENST00000704653.1",
"protein_id": "ENSP00000515978.1",
"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": 1219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "XM_005272675.5",
"protein_id": "XP_005272732.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2575,
"cds_start": -4,
"cds_end": null,
"cds_length": 7728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12606,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "XM_047442548.1",
"protein_id": "XP_047298504.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2570,
"cds_start": -4,
"cds_end": null,
"cds_length": 7713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null,
"transcript": "XM_047442550.1",
"protein_id": "XP_047298506.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2554,
"cds_start": -4,
"cds_end": null,
"cds_length": 7665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"dbsnp": "rs1555922391",
"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": 0.38999998569488525,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9279999732971191,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.083,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.99,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999988247793601,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000378308.7",
"gene_symbol": "USP9X",
"hgnc_id": 12632,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1763+1G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}