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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-41123718-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=41123718&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 41123718,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001410748.1",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "NM_001039591.3",
"protein_id": "NP_001034680.2",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2554,
"cds_start": 90,
"cds_end": null,
"cds_length": 7665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000378308.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001039591.3"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "ENST00000378308.7",
"protein_id": "ENSP00000367558.2",
"transcript_support_level": 5,
"aa_start": 30,
"aa_end": null,
"aa_length": 2554,
"cds_start": 90,
"cds_end": null,
"cds_length": 7665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001039591.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378308.7"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "NM_001410748.1",
"protein_id": "NP_001397677.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2575,
"cds_start": 90,
"cds_end": null,
"cds_length": 7728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001410748.1"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "ENST00000703987.1",
"protein_id": "ENSP00000515604.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2575,
"cds_start": 90,
"cds_end": null,
"cds_length": 7728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000703987.1"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "NM_001039590.3",
"protein_id": "NP_001034679.2",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2570,
"cds_start": 90,
"cds_end": null,
"cds_length": 7713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001039590.3"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "ENST00000324545.9",
"protein_id": "ENSP00000316357.6",
"transcript_support_level": 5,
"aa_start": 30,
"aa_end": null,
"aa_length": 2570,
"cds_start": 90,
"cds_end": null,
"cds_length": 7713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000324545.9"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "NM_001410749.1",
"protein_id": "NP_001397678.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2559,
"cds_start": 90,
"cds_end": null,
"cds_length": 7680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001410749.1"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "NM_001437534.1",
"protein_id": "NP_001424463.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2559,
"cds_start": 90,
"cds_end": null,
"cds_length": 7680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001437534.1"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "ENST00000703986.1",
"protein_id": "ENSP00000515603.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2559,
"cds_start": 90,
"cds_end": null,
"cds_length": 7680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000703986.1"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "ENST00000704650.1",
"protein_id": "ENSP00000515975.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2554,
"cds_start": 90,
"cds_end": null,
"cds_length": 7665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000704650.1"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "ENST00000929529.1",
"protein_id": "ENSP00000599588.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2554,
"cds_start": 90,
"cds_end": null,
"cds_length": 7665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929529.1"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "ENST00000971820.1",
"protein_id": "ENSP00000641879.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2554,
"cds_start": 90,
"cds_end": null,
"cds_length": 7665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971820.1"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "ENST00000704651.1",
"protein_id": "ENSP00000515976.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2503,
"cds_start": 90,
"cds_end": null,
"cds_length": 7512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000704651.1"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "ENST00000704649.1",
"protein_id": "ENSP00000515974.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 1273,
"cds_start": 90,
"cds_end": null,
"cds_length": 3822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000704649.1"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "XM_005272675.5",
"protein_id": "XP_005272732.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2575,
"cds_start": 90,
"cds_end": null,
"cds_length": 7728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005272675.5"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "XM_047442548.1",
"protein_id": "XP_047298504.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2570,
"cds_start": 90,
"cds_end": null,
"cds_length": 7713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442548.1"
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His",
"transcript": "XM_047442550.1",
"protein_id": "XP_047298506.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 2554,
"cds_start": 90,
"cds_end": null,
"cds_length": 7665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442550.1"
}
],
"gene_symbol": "USP9X",
"gene_hgnc_id": 12632,
"dbsnp": "rs754357906",
"frequency_reference_population": 0.000014893795,
"hom_count_reference_population": 8,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.0000145914,
"gnomad_genomes_af": 0.0000178543,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.27589112520217896,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.249,
"revel_prediction": "Benign",
"alphamissense_score": 0.1678,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.507,
"phylop100way_prediction": "Uncertain_significance",
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001410748.1",
"gene_symbol": "USP9X",
"hgnc_id": 12632,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.90G>C",
"hgvs_p": "p.Gln30His"
}
],
"clinvar_disease": "Developmental delay,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Developmental delay|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}