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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: 3-53228076-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=53228076&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 53228076,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001064.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "c.1553C>T",
"hgvs_p": "p.Ala518Val",
"transcript": "NM_001064.4",
"protein_id": "NP_001055.1",
"transcript_support_level": null,
"aa_start": 518,
"aa_end": null,
"aa_length": 623,
"cds_start": 1553,
"cds_end": null,
"cds_length": 1872,
"cdna_start": 1633,
"cdna_end": null,
"cdna_length": 2996,
"mane_select": "ENST00000462138.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "c.1553C>T",
"hgvs_p": "p.Ala518Val",
"transcript": "ENST00000462138.6",
"protein_id": "ENSP00000417773.1",
"transcript_support_level": 1,
"aa_start": 518,
"aa_end": null,
"aa_length": 623,
"cds_start": 1553,
"cds_end": null,
"cds_length": 1872,
"cdna_start": 1633,
"cdna_end": null,
"cdna_length": 2996,
"mane_select": "NM_001064.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "c.1553C>T",
"hgvs_p": "p.Ala518Val",
"transcript": "ENST00000423525.6",
"protein_id": "ENSP00000405455.2",
"transcript_support_level": 1,
"aa_start": 518,
"aa_end": null,
"aa_length": 623,
"cds_start": 1553,
"cds_end": null,
"cds_length": 1872,
"cdna_start": 1611,
"cdna_end": null,
"cdna_length": 2831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "c.1577C>T",
"hgvs_p": "p.Ala526Val",
"transcript": "NM_001258028.2",
"protein_id": "NP_001244957.1",
"transcript_support_level": null,
"aa_start": 526,
"aa_end": null,
"aa_length": 631,
"cds_start": 1577,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 1657,
"cdna_end": null,
"cdna_length": 3020,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "c.1577C>T",
"hgvs_p": "p.Ala526Val",
"transcript": "ENST00000423516.5",
"protein_id": "ENSP00000391481.1",
"transcript_support_level": 2,
"aa_start": 526,
"aa_end": null,
"aa_length": 631,
"cds_start": 1577,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 1657,
"cdna_end": null,
"cdna_length": 2075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "c.1553C>T",
"hgvs_p": "p.Ala518Val",
"transcript": "NM_001135055.3",
"protein_id": "NP_001128527.1",
"transcript_support_level": null,
"aa_start": 518,
"aa_end": null,
"aa_length": 623,
"cds_start": 1553,
"cds_end": null,
"cds_length": 1872,
"cdna_start": 1633,
"cdna_end": null,
"cdna_length": 2855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "c.1577C>T",
"hgvs_p": "p.Ala526Val",
"transcript": "XM_011534054.2",
"protein_id": "XP_011532356.1",
"transcript_support_level": null,
"aa_start": 526,
"aa_end": null,
"aa_length": 631,
"cds_start": 1577,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 1657,
"cdna_end": null,
"cdna_length": 2879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "n.*981C>T",
"hgvs_p": null,
"transcript": "ENST00000450814.6",
"protein_id": "ENSP00000413503.2",
"transcript_support_level": 2,
"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": 1941,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "n.4862C>T",
"hgvs_p": null,
"transcript": "ENST00000460343.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 7286,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "n.1554C>T",
"hgvs_p": null,
"transcript": "ENST00000461139.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 1972,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "n.1523C>T",
"hgvs_p": null,
"transcript": "NR_047580.2",
"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": 2886,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "n.*981C>T",
"hgvs_p": null,
"transcript": "ENST00000450814.6",
"protein_id": "ENSP00000413503.2",
"transcript_support_level": 2,
"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": 1941,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"hgvs_c": "n.*481+200C>T",
"hgvs_p": null,
"transcript": "ENST00000469678.1",
"protein_id": "ENSP00000418340.1",
"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": 1871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TKT",
"gene_hgnc_id": 11834,
"dbsnp": "rs1328734845",
"frequency_reference_population": 0.000009300203,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.0000082157,
"gnomad_genomes_af": 0.0000197044,
"gnomad_exomes_ac": 12,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8508211374282837,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.694,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4878,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.19,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.889,
"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": 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_001064.4",
"gene_symbol": "TKT",
"hgnc_id": 11834,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1553C>T",
"hgvs_p": "p.Ala518Val"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}