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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: 2-31373872-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=31373872&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 31373872,
"ref": "C",
"alt": "G",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_000379.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.1686+1G>C",
"hgvs_p": null,
"transcript": "NM_000379.4",
"protein_id": "NP_000370.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1333,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.1686+1G>C",
"hgvs_p": null,
"transcript": "ENST00000379416.4",
"protein_id": "ENSP00000368727.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1333,
"cds_start": null,
"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": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.1687G>C",
"hgvs_p": "p.Val563Leu",
"transcript": "ENST00000879524.1",
"protein_id": "ENSP00000549583.1",
"transcript_support_level": null,
"aa_start": 563,
"aa_end": null,
"aa_length": 1336,
"cds_start": 1687,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.1794+1G>C",
"hgvs_p": null,
"transcript": "ENST00000879520.1",
"protein_id": "ENSP00000549579.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1369,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.1683+1G>C",
"hgvs_p": null,
"transcript": "ENST00000879522.1",
"protein_id": "ENSP00000549581.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1332,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.1686+1G>C",
"hgvs_p": null,
"transcript": "ENST00000879523.1",
"protein_id": "ENSP00000549582.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1313,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.1686+1G>C",
"hgvs_p": null,
"transcript": "ENST00000879525.1",
"protein_id": "ENSP00000549584.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1310,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.1686+1G>C",
"hgvs_p": null,
"transcript": "ENST00000879521.1",
"protein_id": "ENSP00000549580.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1274,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.1080+1G>C",
"hgvs_p": null,
"transcript": "ENST00000879526.1",
"protein_id": "ENSP00000549585.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1131,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.1683+1G>C",
"hgvs_p": null,
"transcript": "XM_011533095.3",
"protein_id": "XP_011531397.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1332,
"cds_start": null,
"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"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.1686+1G>C",
"hgvs_p": null,
"transcript": "XM_011533096.3",
"protein_id": "XP_011531398.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1053,
"cds_start": null,
"cds_end": null,
"cds_length": 3162,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533096.3"
}
],
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"dbsnp": "rs148412639",
"frequency_reference_population": 0.00092517544,
"hom_count_reference_population": 2,
"allele_count_reference_population": 1493,
"gnomad_exomes_af": 0.000962049,
"gnomad_genomes_af": 0.000571301,
"gnomad_exomes_ac": 1406,
"gnomad_genomes_ac": 87,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3799999952316284,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9380000233650208,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.38,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.681,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 1,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999990361384395,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PP5,BS1_Supporting",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 1,
"pathogenic_score": 3,
"criteria": [
"PVS1_Moderate",
"PP5",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000379.4",
"gene_symbol": "XDH",
"hgnc_id": 12805,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1686+1G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Hereditary xanthinuria type 1,XDH-related disorder,Xanthinuria type II,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:4 US:2",
"phenotype_combined": "Hereditary xanthinuria type 1|Xanthinuria type II|not provided|XDH-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}