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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-123900661-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=123900661&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 123900661,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000371199.8",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "c.1268A>C",
"hgvs_p": "p.Gln423Pro",
"transcript": "NM_001167.4",
"protein_id": "NP_001158.2",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 497,
"cds_start": 1268,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1541,
"cdna_end": null,
"cdna_length": 8558,
"mane_select": "ENST00000371199.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "c.1268A>C",
"hgvs_p": "p.Gln423Pro",
"transcript": "ENST00000371199.8",
"protein_id": "ENSP00000360242.3",
"transcript_support_level": 1,
"aa_start": 423,
"aa_end": null,
"aa_length": 497,
"cds_start": 1268,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1541,
"cdna_end": null,
"cdna_length": 8558,
"mane_select": "NM_001167.4",
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "n.490A>C",
"hgvs_p": null,
"transcript": "ENST00000497640.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "c.1268A>C",
"hgvs_p": "p.Gln423Pro",
"transcript": "NM_001204401.2",
"protein_id": "NP_001191330.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 497,
"cds_start": 1268,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1392,
"cdna_end": null,
"cdna_length": 8409,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "c.1268A>C",
"hgvs_p": "p.Gln423Pro",
"transcript": "NM_001378590.1",
"protein_id": "NP_001365519.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 497,
"cds_start": 1268,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1396,
"cdna_end": null,
"cdna_length": 8413,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "c.1268A>C",
"hgvs_p": "p.Gln423Pro",
"transcript": "NM_001378591.1",
"protein_id": "NP_001365520.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 497,
"cds_start": 1268,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1519,
"cdna_end": null,
"cdna_length": 8536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "c.1268A>C",
"hgvs_p": "p.Gln423Pro",
"transcript": "NM_001378592.1",
"protein_id": "NP_001365521.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 497,
"cds_start": 1268,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1331,
"cdna_end": null,
"cdna_length": 8348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "c.1268A>C",
"hgvs_p": "p.Gln423Pro",
"transcript": "ENST00000355640.3",
"protein_id": "ENSP00000347858.3",
"transcript_support_level": 5,
"aa_start": 423,
"aa_end": null,
"aa_length": 497,
"cds_start": 1268,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1574,
"cdna_end": null,
"cdna_length": 8584,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "c.1268A>C",
"hgvs_p": "p.Gln423Pro",
"transcript": "ENST00000422098.6",
"protein_id": "ENSP00000405529.2",
"transcript_support_level": 4,
"aa_start": 423,
"aa_end": null,
"aa_length": 497,
"cds_start": 1268,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1519,
"cdna_end": null,
"cdna_length": 3735,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "n.468A>C",
"hgvs_p": null,
"transcript": "ENST00000468691.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 764,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "n.533A>C",
"hgvs_p": null,
"transcript": "ENST00000481776.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 598,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "n.713A>C",
"hgvs_p": null,
"transcript": "ENST00000698505.1",
"protein_id": null,
"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": 1616,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "n.632A>C",
"hgvs_p": null,
"transcript": "NR_037916.2",
"protein_id": null,
"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": 7649,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "n.614A>C",
"hgvs_p": null,
"transcript": "NR_165803.1",
"protein_id": null,
"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": 7631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"hgvs_c": "n.*95A>C",
"hgvs_p": null,
"transcript": "ENST00000497906.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "XIAP",
"gene_hgnc_id": 592,
"dbsnp": "rs5956583",
"frequency_reference_population": 0.3589556,
"hom_count_reference_population": 194575,
"allele_count_reference_population": 433707,
"gnomad_exomes_af": 0.356884,
"gnomad_genomes_af": 0.37954,
"gnomad_exomes_ac": 391786,
"gnomad_genomes_ac": 41921,
"gnomad_exomes_homalt": 49325,
"gnomad_genomes_homalt": 6055,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0029205679893493652,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.081,
"revel_prediction": "Benign",
"alphamissense_score": 0.07,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.701,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000371199.8",
"gene_symbol": "XIAP",
"hgnc_id": 592,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1268A>C",
"hgvs_p": "p.Gln423Pro"
}
],
"clinvar_disease": "Autoinflammatory syndrome,X-linked lymphoproliferative disease due to XIAP deficiency,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:12 O:1",
"phenotype_combined": "not specified|X-linked lymphoproliferative disease due to XIAP deficiency|not provided|Autoinflammatory syndrome",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}