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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-41219135-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=41219135&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 41219135,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000378308.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6469C>A",
"hgvs_p": "p.Leu2157Ile",
"transcript": "NM_001039591.3",
"protein_id": "NP_001034680.2",
"transcript_support_level": null,
"aa_start": 2157,
"aa_end": null,
"aa_length": 2554,
"cds_start": 6469,
"cds_end": null,
"cds_length": 7665,
"cdna_start": 7292,
"cdna_end": null,
"cdna_length": 12543,
"mane_select": "ENST00000378308.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6469C>A",
"hgvs_p": "p.Leu2157Ile",
"transcript": "ENST00000378308.7",
"protein_id": "ENSP00000367558.2",
"transcript_support_level": 5,
"aa_start": 2157,
"aa_end": null,
"aa_length": 2554,
"cds_start": 6469,
"cds_end": null,
"cds_length": 7665,
"cdna_start": 7292,
"cdna_end": null,
"cdna_length": 12543,
"mane_select": "NM_001039591.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6484C>A",
"hgvs_p": "p.Leu2162Ile",
"transcript": "NM_001410748.1",
"protein_id": "NP_001397677.1",
"transcript_support_level": null,
"aa_start": 2162,
"aa_end": null,
"aa_length": 2575,
"cds_start": 6484,
"cds_end": null,
"cds_length": 7728,
"cdna_start": 7356,
"cdna_end": null,
"cdna_length": 12655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6484C>A",
"hgvs_p": "p.Leu2162Ile",
"transcript": "ENST00000703987.1",
"protein_id": "ENSP00000515604.1",
"transcript_support_level": null,
"aa_start": 2162,
"aa_end": null,
"aa_length": 2575,
"cds_start": 6484,
"cds_end": null,
"cds_length": 7728,
"cdna_start": 6904,
"cdna_end": null,
"cdna_length": 8383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6469C>A",
"hgvs_p": "p.Leu2157Ile",
"transcript": "NM_001039590.3",
"protein_id": "NP_001034679.2",
"transcript_support_level": null,
"aa_start": 2157,
"aa_end": null,
"aa_length": 2570,
"cds_start": 6469,
"cds_end": null,
"cds_length": 7713,
"cdna_start": 7292,
"cdna_end": null,
"cdna_length": 12591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6469C>A",
"hgvs_p": "p.Leu2157Ile",
"transcript": "ENST00000324545.9",
"protein_id": "ENSP00000316357.6",
"transcript_support_level": 5,
"aa_start": 2157,
"aa_end": null,
"aa_length": 2570,
"cds_start": 6469,
"cds_end": null,
"cds_length": 7713,
"cdna_start": 7292,
"cdna_end": null,
"cdna_length": 12591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6484C>A",
"hgvs_p": "p.Leu2162Ile",
"transcript": "NM_001410749.1",
"protein_id": "NP_001397678.1",
"transcript_support_level": null,
"aa_start": 2162,
"aa_end": null,
"aa_length": 2559,
"cds_start": 6484,
"cds_end": null,
"cds_length": 7680,
"cdna_start": 7356,
"cdna_end": null,
"cdna_length": 12607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6484C>A",
"hgvs_p": "p.Leu2162Ile",
"transcript": "NM_001437534.1",
"protein_id": "NP_001424463.1",
"transcript_support_level": null,
"aa_start": 2162,
"aa_end": null,
"aa_length": 2559,
"cds_start": 6484,
"cds_end": null,
"cds_length": 7680,
"cdna_start": 7307,
"cdna_end": null,
"cdna_length": 12558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6484C>A",
"hgvs_p": "p.Leu2162Ile",
"transcript": "ENST00000703986.1",
"protein_id": "ENSP00000515603.1",
"transcript_support_level": null,
"aa_start": 2162,
"aa_end": null,
"aa_length": 2559,
"cds_start": 6484,
"cds_end": null,
"cds_length": 7680,
"cdna_start": 7286,
"cdna_end": null,
"cdna_length": 12490,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6469C>A",
"hgvs_p": "p.Leu2157Ile",
"transcript": "ENST00000704650.1",
"protein_id": "ENSP00000515975.1",
"transcript_support_level": null,
"aa_start": 2157,
"aa_end": null,
"aa_length": 2554,
"cds_start": 6469,
"cds_end": null,
"cds_length": 7665,
"cdna_start": 6911,
"cdna_end": null,
"cdna_length": 9555,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6316C>A",
"hgvs_p": "p.Leu2106Ile",
"transcript": "ENST00000704651.1",
"protein_id": "ENSP00000515976.1",
"transcript_support_level": null,
"aa_start": 2106,
"aa_end": null,
"aa_length": 2503,
"cds_start": 6316,
"cds_end": null,
"cds_length": 7512,
"cdna_start": 6644,
"cdna_end": null,
"cdna_length": 9282,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.3421C>A",
"hgvs_p": "p.Leu1141Ile",
"transcript": "ENST00000704654.1",
"protein_id": "ENSP00000515979.1",
"transcript_support_level": null,
"aa_start": 1141,
"aa_end": null,
"aa_length": 1513,
"cds_start": 3421,
"cds_end": null,
"cds_length": 4542,
"cdna_start": 3423,
"cdna_end": null,
"cdna_length": 5993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6484C>A",
"hgvs_p": "p.Leu2162Ile",
"transcript": "XM_005272675.5",
"protein_id": "XP_005272732.1",
"transcript_support_level": null,
"aa_start": 2162,
"aa_end": null,
"aa_length": 2575,
"cds_start": 6484,
"cds_end": null,
"cds_length": 7728,
"cdna_start": 7307,
"cdna_end": null,
"cdna_length": 12606,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6469C>A",
"hgvs_p": "p.Leu2157Ile",
"transcript": "XM_047442548.1",
"protein_id": "XP_047298504.1",
"transcript_support_level": null,
"aa_start": 2157,
"aa_end": null,
"aa_length": 2570,
"cds_start": 6469,
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"cdna_start": 7341,
"cdna_end": null,
"cdna_length": 12640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.6469C>A",
"hgvs_p": "p.Leu2157Ile",
"transcript": "XM_047442550.1",
"protein_id": "XP_047298506.1",
"transcript_support_level": null,
"aa_start": 2157,
"aa_end": null,
"aa_length": 2554,
"cds_start": 6469,
"cds_end": null,
"cds_length": 7665,
"cdna_start": 7341,
"cdna_end": null,
"cdna_length": 12592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "n.*3146C>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,
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"cdna_start": null,
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"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "n.*1397C>A",
"hgvs_p": null,
"transcript": "ENST00000704655.1",
"protein_id": "ENSP00000515980.1",
"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": 7863,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "n.*1125C>A",
"hgvs_p": null,
"transcript": "ENST00000704656.1",
"protein_id": "ENSP00000515981.1",
"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": 7171,
"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": 30,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "n.*3146C>A",
"hgvs_p": null,
"transcript": "ENST00000704652.1",
"protein_id": "ENSP00000515977.1",
"transcript_support_level": null,
"aa_start": null,
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"cdna_start": null,
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"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": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "n.*1397C>A",
"hgvs_p": null,
"transcript": "ENST00000704655.1",
"protein_id": "ENSP00000515980.1",
"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": 7863,
"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": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "n.*1125C>A",
"hgvs_p": null,
"transcript": "ENST00000704656.1",
"protein_id": "ENSP00000515981.1",
"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": 7171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.3685-13252C>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
}
],
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"dbsnp": "rs587777319",
"frequency_reference_population": 0.0000033104088,
"hom_count_reference_population": 1,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000182435,
"gnomad_genomes_af": 0.0000178527,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5489621162414551,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.129,
"revel_prediction": "Benign",
"alphamissense_score": 0.1873,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.876,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000378308.7",
"gene_symbol": "USP9X",
"hgnc_id": 12632,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.6469C>A",
"hgvs_p": "p.Leu2157Ile"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}