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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: 2-31342214-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=31342214&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 31342214,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000379.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3488T>C",
"hgvs_p": "p.Val1163Ala",
"transcript": "NM_000379.4",
"protein_id": "NP_000370.2",
"transcript_support_level": null,
"aa_start": 1163,
"aa_end": null,
"aa_length": 1333,
"cds_start": 3488,
"cds_end": null,
"cds_length": 4002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000379416.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000379.4"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3488T>C",
"hgvs_p": "p.Val1163Ala",
"transcript": "ENST00000379416.4",
"protein_id": "ENSP00000368727.3",
"transcript_support_level": 1,
"aa_start": 1163,
"aa_end": null,
"aa_length": 1333,
"cds_start": 3488,
"cds_end": null,
"cds_length": 4002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000379.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379416.4"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3596T>C",
"hgvs_p": "p.Val1199Ala",
"transcript": "ENST00000879520.1",
"protein_id": "ENSP00000549579.1",
"transcript_support_level": null,
"aa_start": 1199,
"aa_end": null,
"aa_length": 1369,
"cds_start": 3596,
"cds_end": null,
"cds_length": 4110,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879520.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3497T>C",
"hgvs_p": "p.Val1166Ala",
"transcript": "ENST00000879524.1",
"protein_id": "ENSP00000549583.1",
"transcript_support_level": null,
"aa_start": 1166,
"aa_end": null,
"aa_length": 1336,
"cds_start": 3497,
"cds_end": null,
"cds_length": 4011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879524.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3485T>C",
"hgvs_p": "p.Val1162Ala",
"transcript": "ENST00000879522.1",
"protein_id": "ENSP00000549581.1",
"transcript_support_level": null,
"aa_start": 1162,
"aa_end": null,
"aa_length": 1332,
"cds_start": 3485,
"cds_end": null,
"cds_length": 3999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879522.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3428T>C",
"hgvs_p": "p.Val1143Ala",
"transcript": "ENST00000879523.1",
"protein_id": "ENSP00000549582.1",
"transcript_support_level": null,
"aa_start": 1143,
"aa_end": null,
"aa_length": 1313,
"cds_start": 3428,
"cds_end": null,
"cds_length": 3942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879523.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3419T>C",
"hgvs_p": "p.Val1140Ala",
"transcript": "ENST00000879525.1",
"protein_id": "ENSP00000549584.1",
"transcript_support_level": null,
"aa_start": 1140,
"aa_end": null,
"aa_length": 1310,
"cds_start": 3419,
"cds_end": null,
"cds_length": 3933,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879525.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3488T>C",
"hgvs_p": "p.Val1163Ala",
"transcript": "ENST00000879521.1",
"protein_id": "ENSP00000549580.1",
"transcript_support_level": null,
"aa_start": 1163,
"aa_end": null,
"aa_length": 1274,
"cds_start": 3488,
"cds_end": null,
"cds_length": 3825,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879521.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.2882T>C",
"hgvs_p": "p.Val961Ala",
"transcript": "ENST00000879526.1",
"protein_id": "ENSP00000549585.1",
"transcript_support_level": null,
"aa_start": 961,
"aa_end": null,
"aa_length": 1131,
"cds_start": 2882,
"cds_end": null,
"cds_length": 3396,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879526.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3485T>C",
"hgvs_p": "p.Val1162Ala",
"transcript": "XM_011533095.3",
"protein_id": "XP_011531397.1",
"transcript_support_level": null,
"aa_start": 1162,
"aa_end": null,
"aa_length": 1332,
"cds_start": 3485,
"cds_end": null,
"cds_length": 3999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533095.3"
}
],
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"dbsnp": "rs142988357",
"frequency_reference_population": 0.000012997336,
"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.0000129973,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8862084150314331,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.723,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4098,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.038,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.04,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000379.4",
"gene_symbol": "XDH",
"hgnc_id": 12805,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3488T>C",
"hgvs_p": "p.Val1163Ala"
}
],
"clinvar_disease": "Hereditary xanthinuria type 1,Xanthinuria type II",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Xanthinuria type II|Hereditary xanthinuria type 1",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}