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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-41168136-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=41168136&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"effects": [
"stop_gained"
],
"gene_symbol": "USP9X",
"hgnc_id": 12632,
"hgvs_c": "c.2569C>T",
"hgvs_p": "p.Arg857*",
"inheritance_mode": "XL",
"pathogenic_score": 11,
"score": 11,
"transcript": "NM_001410748.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_score": 11,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.5,
"chr": "X",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " X-linked 99, female-restricted, syndromic,Intellectual disability",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.5,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2554,
"aa_ref": "R",
"aa_start": 852,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12543,
"cdna_start": 3377,
"cds_end": null,
"cds_length": 7665,
"cds_start": 2554,
"consequences": [
"stop_gained"
],
"exon_count": 45,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_001039591.3",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2554C>T",
"hgvs_p": "p.Arg852*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000378308.7",
"protein_coding": true,
"protein_id": "NP_001034680.2",
"strand": true,
"transcript": "NM_001039591.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2554,
"aa_ref": "R",
"aa_start": 852,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 12543,
"cdna_start": 3377,
"cds_end": null,
"cds_length": 7665,
"cds_start": 2554,
"consequences": [
"stop_gained"
],
"exon_count": 45,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000378308.7",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2554C>T",
"hgvs_p": "p.Arg852*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001039591.3",
"protein_coding": true,
"protein_id": "ENSP00000367558.2",
"strand": true,
"transcript": "ENST00000378308.7",
"transcript_support_level": 5
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2575,
"aa_ref": "R",
"aa_start": 857,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12655,
"cdna_start": 3441,
"cds_end": null,
"cds_length": 7728,
"cds_start": 2569,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_001410748.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2569C>T",
"hgvs_p": "p.Arg857*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001397677.1",
"strand": true,
"transcript": "NM_001410748.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2575,
"aa_ref": "R",
"aa_start": 857,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8383,
"cdna_start": 2989,
"cds_end": null,
"cds_length": 7728,
"cds_start": 2569,
"consequences": [
"stop_gained"
],
"exon_count": 45,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000703987.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2569C>T",
"hgvs_p": "p.Arg857*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515604.1",
"strand": true,
"transcript": "ENST00000703987.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2570,
"aa_ref": "R",
"aa_start": 852,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12591,
"cdna_start": 3377,
"cds_end": null,
"cds_length": 7713,
"cds_start": 2554,
"consequences": [
"stop_gained"
],
"exon_count": 45,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_001039590.3",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2554C>T",
"hgvs_p": "p.Arg852*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001034679.2",
"strand": true,
"transcript": "NM_001039590.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2570,
"aa_ref": "R",
"aa_start": 852,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12591,
"cdna_start": 3377,
"cds_end": null,
"cds_length": 7713,
"cds_start": 2554,
"consequences": [
"stop_gained"
],
"exon_count": 45,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000324545.9",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2554C>T",
"hgvs_p": "p.Arg852*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000316357.6",
"strand": true,
"transcript": "ENST00000324545.9",
"transcript_support_level": 5
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2559,
"aa_ref": "R",
"aa_start": 857,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12607,
"cdna_start": 3441,
"cds_end": null,
"cds_length": 7680,
"cds_start": 2569,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_001410749.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2569C>T",
"hgvs_p": "p.Arg857*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001397678.1",
"strand": true,
"transcript": "NM_001410749.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2559,
"aa_ref": "R",
"aa_start": 857,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12558,
"cdna_start": 3392,
"cds_end": null,
"cds_length": 7680,
"cds_start": 2569,
"consequences": [
"stop_gained"
],
"exon_count": 45,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_001437534.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2569C>T",
"hgvs_p": "p.Arg857*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001424463.1",
"strand": true,
"transcript": "NM_001437534.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2559,
"aa_ref": "R",
"aa_start": 857,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12490,
"cdna_start": 3371,
"cds_end": null,
"cds_length": 7680,
"cds_start": 2569,
"consequences": [
"stop_gained"
],
"exon_count": 45,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000703986.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2569C>T",
"hgvs_p": "p.Arg857*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515603.1",
"strand": true,
"transcript": "ENST00000703986.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2554,
"aa_ref": "R",
"aa_start": 852,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9555,
"cdna_start": 2996,
"cds_end": null,
"cds_length": 7665,
"cds_start": 2554,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000704650.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2554C>T",
"hgvs_p": "p.Arg852*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515975.1",
"strand": true,
"transcript": "ENST00000704650.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2554,
"aa_ref": "R",
"aa_start": 852,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9010,
"cdna_start": 3675,
"cds_end": null,
"cds_length": 7665,
"cds_start": 2554,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000929529.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2554C>T",
"hgvs_p": "p.Arg852*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599588.1",
"strand": true,
"transcript": "ENST00000929529.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2554,
"aa_ref": "R",
"aa_start": 852,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8997,
"cdna_start": 3484,
"cds_end": null,
"cds_length": 7665,
"cds_start": 2554,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000971820.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2554C>T",
"hgvs_p": "p.Arg852*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641879.1",
"strand": true,
"transcript": "ENST00000971820.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2503,
"aa_ref": "R",
"aa_start": 801,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9282,
"cdna_start": 2729,
"cds_end": null,
"cds_length": 7512,
"cds_start": 2401,
"consequences": [
"stop_gained"
],
"exon_count": 44,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000704651.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2401C>T",
"hgvs_p": "p.Arg801*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515976.1",
"strand": true,
"transcript": "ENST00000704651.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1273,
"aa_ref": "R",
"aa_start": 852,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8700,
"cdna_start": 3377,
"cds_end": null,
"cds_length": 3822,
"cds_start": 2554,
"consequences": [
"stop_gained"
],
"exon_count": 25,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000704649.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2554C>T",
"hgvs_p": "p.Arg852*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515974.1",
"strand": true,
"transcript": "ENST00000704649.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2575,
"aa_ref": "R",
"aa_start": 857,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12606,
"cdna_start": 3392,
"cds_end": null,
"cds_length": 7728,
"cds_start": 2569,
"consequences": [
"stop_gained"
],
"exon_count": 45,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_005272675.5",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2569C>T",
"hgvs_p": "p.Arg857*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005272732.1",
"strand": true,
"transcript": "XM_005272675.5",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2570,
"aa_ref": "R",
"aa_start": 852,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12640,
"cdna_start": 3426,
"cds_end": null,
"cds_length": 7713,
"cds_start": 2554,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047442548.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2554C>T",
"hgvs_p": "p.Arg852*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047298504.1",
"strand": true,
"transcript": "XM_047442548.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2554,
"aa_ref": "R",
"aa_start": 852,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12592,
"cdna_start": 3426,
"cds_end": null,
"cds_length": 7665,
"cds_start": 2554,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047442550.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "c.2554C>T",
"hgvs_p": "p.Arg852*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047298506.1",
"strand": true,
"transcript": "XM_047442550.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 669,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000467173.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "n.563C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000467173.1",
"transcript_support_level": 3
},
{
"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": 10819,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 37,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000704652.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "n.1783C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000515977.1",
"strand": true,
"transcript": "ENST00000704652.1",
"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": 1219,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000704653.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "n.*752C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000515978.1",
"strand": true,
"transcript": "ENST00000704653.1",
"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": 1219,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000704653.1",
"gene_hgnc_id": 12632,
"gene_symbol": "USP9X",
"hgvs_c": "n.*752C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
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],
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]
}