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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: 2-31339546-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=31339546&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 31339546,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_000379.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3717G>A",
"hgvs_p": "p.Glu1239Glu",
"transcript": "NM_000379.4",
"protein_id": "NP_000370.2",
"transcript_support_level": null,
"aa_start": 1239,
"aa_end": null,
"aa_length": 1333,
"cds_start": 3717,
"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": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3717G>A",
"hgvs_p": "p.Glu1239Glu",
"transcript": "ENST00000379416.4",
"protein_id": "ENSP00000368727.3",
"transcript_support_level": 1,
"aa_start": 1239,
"aa_end": null,
"aa_length": 1333,
"cds_start": 3717,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3825G>A",
"hgvs_p": "p.Glu1275Glu",
"transcript": "ENST00000879520.1",
"protein_id": "ENSP00000549579.1",
"transcript_support_level": null,
"aa_start": 1275,
"aa_end": null,
"aa_length": 1369,
"cds_start": 3825,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3726G>A",
"hgvs_p": "p.Glu1242Glu",
"transcript": "ENST00000879524.1",
"protein_id": "ENSP00000549583.1",
"transcript_support_level": null,
"aa_start": 1242,
"aa_end": null,
"aa_length": 1336,
"cds_start": 3726,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3714G>A",
"hgvs_p": "p.Glu1238Glu",
"transcript": "ENST00000879522.1",
"protein_id": "ENSP00000549581.1",
"transcript_support_level": null,
"aa_start": 1238,
"aa_end": null,
"aa_length": 1332,
"cds_start": 3714,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3657G>A",
"hgvs_p": "p.Glu1219Glu",
"transcript": "ENST00000879523.1",
"protein_id": "ENSP00000549582.1",
"transcript_support_level": null,
"aa_start": 1219,
"aa_end": null,
"aa_length": 1313,
"cds_start": 3657,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3648G>A",
"hgvs_p": "p.Glu1216Glu",
"transcript": "ENST00000879525.1",
"protein_id": "ENSP00000549584.1",
"transcript_support_level": null,
"aa_start": 1216,
"aa_end": null,
"aa_length": 1310,
"cds_start": 3648,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3717G>A",
"hgvs_p": "p.Glu1239Glu",
"transcript": "ENST00000879521.1",
"protein_id": "ENSP00000549580.1",
"transcript_support_level": null,
"aa_start": 1239,
"aa_end": null,
"aa_length": 1274,
"cds_start": 3717,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3111G>A",
"hgvs_p": "p.Glu1037Glu",
"transcript": "ENST00000879526.1",
"protein_id": "ENSP00000549585.1",
"transcript_support_level": null,
"aa_start": 1037,
"aa_end": null,
"aa_length": 1131,
"cds_start": 3111,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XDH",
"gene_hgnc_id": 12805,
"hgvs_c": "c.3714G>A",
"hgvs_p": "p.Glu1238Glu",
"transcript": "XM_011533095.3",
"protein_id": "XP_011531397.1",
"transcript_support_level": null,
"aa_start": 1238,
"aa_end": null,
"aa_length": 1332,
"cds_start": 3714,
"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": "rs207440",
"frequency_reference_population": 0.057487458,
"hom_count_reference_population": 2861,
"allele_count_reference_population": 92792,
"gnomad_exomes_af": 0.058026,
"gnomad_genomes_af": 0.052316,
"gnomad_exomes_ac": 84827,
"gnomad_genomes_ac": 7965,
"gnomad_exomes_homalt": 2631,
"gnomad_genomes_homalt": 230,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3499999940395355,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.552,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_000379.4",
"gene_symbol": "XDH",
"hgnc_id": 12805,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3717G>A",
"hgvs_p": "p.Glu1239Glu"
}
],
"clinvar_disease": "Hereditary xanthinuria type 1,Xanthinuria type II,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|Hereditary xanthinuria type 1|not provided|Xanthinuria type II",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}