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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: 17-3664723-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=3664723&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 3664723,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_014604.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TAX1BP3",
"gene_hgnc_id": 30684,
"hgvs_c": "c.115C>G",
"hgvs_p": "p.Gln39Glu",
"transcript": "NM_014604.4",
"protein_id": "NP_055419.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 124,
"cds_start": 115,
"cds_end": null,
"cds_length": 375,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000225525.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014604.4"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TAX1BP3",
"gene_hgnc_id": 30684,
"hgvs_c": "c.115C>G",
"hgvs_p": "p.Gln39Glu",
"transcript": "ENST00000225525.4",
"protein_id": "ENSP00000225525.3",
"transcript_support_level": 1,
"aa_start": 39,
"aa_end": null,
"aa_length": 124,
"cds_start": 115,
"cds_end": null,
"cds_length": 375,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014604.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000225525.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P2RX5-TAX1BP3",
"gene_hgnc_id": 49191,
"hgvs_c": "n.*3472C>G",
"hgvs_p": null,
"transcript": "ENST00000550383.1",
"protein_id": "ENSP00000455681.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000550383.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P2RX5-TAX1BP3",
"gene_hgnc_id": 49191,
"hgvs_c": "n.*3472C>G",
"hgvs_p": null,
"transcript": "ENST00000550383.1",
"protein_id": "ENSP00000455681.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000550383.1"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TAX1BP3",
"gene_hgnc_id": 30684,
"hgvs_c": "c.193C>G",
"hgvs_p": "p.Gln65Glu",
"transcript": "ENST00000874102.1",
"protein_id": "ENSP00000544161.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 150,
"cds_start": 193,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874102.1"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TAX1BP3",
"gene_hgnc_id": 30684,
"hgvs_c": "c.112C>G",
"hgvs_p": "p.Gln38Glu",
"transcript": "ENST00000874103.1",
"protein_id": "ENSP00000544162.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 123,
"cds_start": 112,
"cds_end": null,
"cds_length": 372,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874103.1"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TAX1BP3",
"gene_hgnc_id": 30684,
"hgvs_c": "c.112C>G",
"hgvs_p": "p.Gln38Glu",
"transcript": "ENST00000920138.1",
"protein_id": "ENSP00000590197.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 123,
"cds_start": 112,
"cds_end": null,
"cds_length": 372,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920138.1"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TAX1BP3",
"gene_hgnc_id": 30684,
"hgvs_c": "c.115C>G",
"hgvs_p": "p.Gln39Glu",
"transcript": "NM_001204698.2",
"protein_id": "NP_001191627.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 98,
"cds_start": 115,
"cds_end": null,
"cds_length": 297,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001204698.2"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TAX1BP3",
"gene_hgnc_id": 30684,
"hgvs_c": "c.115C>G",
"hgvs_p": "p.Gln39Glu",
"transcript": "ENST00000611779.4",
"protein_id": "ENSP00000484776.1",
"transcript_support_level": 2,
"aa_start": 39,
"aa_end": null,
"aa_length": 98,
"cds_start": 115,
"cds_end": null,
"cds_length": 297,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000611779.4"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TAX1BP3",
"gene_hgnc_id": 30684,
"hgvs_c": "c.112C>G",
"hgvs_p": "p.Gln38Glu",
"transcript": "ENST00000920139.1",
"protein_id": "ENSP00000590198.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 97,
"cds_start": 112,
"cds_end": null,
"cds_length": 294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920139.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P2RX5-TAX1BP3",
"gene_hgnc_id": 49191,
"hgvs_c": "n.5170C>G",
"hgvs_p": null,
"transcript": "NR_037928.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_037928.1"
}
],
"gene_symbol": "TAX1BP3",
"gene_hgnc_id": 30684,
"dbsnp": "rs142167108",
"frequency_reference_population": 0.00010411025,
"hom_count_reference_population": 0,
"allele_count_reference_population": 168,
"gnomad_exomes_af": 0.000107422,
"gnomad_genomes_af": 0.0000723009,
"gnomad_exomes_ac": 157,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.355299174785614,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.245,
"revel_prediction": "Benign",
"alphamissense_score": 0.6389,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.43,
"phylop100way_prediction": "Pathogenic",
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "NM_014604.4",
"gene_symbol": "TAX1BP3",
"hgnc_id": 30684,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.115C>G",
"hgvs_p": "p.Gln39Glu"
},
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "ENST00000550383.1",
"gene_symbol": "P2RX5-TAX1BP3",
"hgnc_id": 49191,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*3472C>G",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}