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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: 4-82917109-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=82917109&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 82917109,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000302236.10",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"hgvs_c": "c.897G>T",
"hgvs_p": "p.Leu299Phe",
"transcript": "NM_024672.6",
"protein_id": "NP_078948.3",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 903,
"cds_start": 897,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 965,
"cdna_end": null,
"cdna_length": 3825,
"mane_select": "ENST00000302236.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"hgvs_c": "c.897G>T",
"hgvs_p": "p.Leu299Phe",
"transcript": "ENST00000302236.10",
"protein_id": "ENSP00000305533.5",
"transcript_support_level": 1,
"aa_start": 299,
"aa_end": null,
"aa_length": 903,
"cds_start": 897,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 965,
"cdna_end": null,
"cdna_length": 3825,
"mane_select": "NM_024672.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"hgvs_c": "c.465G>T",
"hgvs_p": "p.Leu155Phe",
"transcript": "NM_001317776.2",
"protein_id": "NP_001304705.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 759,
"cds_start": 465,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 1031,
"cdna_end": null,
"cdna_length": 3891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"hgvs_c": "c.936G>T",
"hgvs_p": "p.Leu312Phe",
"transcript": "XM_047416165.1",
"protein_id": "XP_047272121.1",
"transcript_support_level": null,
"aa_start": 312,
"aa_end": null,
"aa_length": 916,
"cds_start": 936,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 3447,
"cdna_end": null,
"cdna_length": 6307,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"hgvs_c": "c.465G>T",
"hgvs_p": "p.Leu155Phe",
"transcript": "XM_047416166.1",
"protein_id": "XP_047272122.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 759,
"cds_start": 465,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 1876,
"cdna_end": null,
"cdna_length": 4736,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"hgvs_c": "c.465G>T",
"hgvs_p": "p.Leu155Phe",
"transcript": "XM_047416167.1",
"protein_id": "XP_047272123.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 759,
"cds_start": 465,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 1256,
"cdna_end": null,
"cdna_length": 4116,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"hgvs_c": "c.465G>T",
"hgvs_p": "p.Leu155Phe",
"transcript": "XM_047416168.1",
"protein_id": "XP_047272124.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 759,
"cds_start": 465,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 710,
"cdna_end": null,
"cdna_length": 3570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"hgvs_c": "c.48G>T",
"hgvs_p": "p.Leu16Phe",
"transcript": "XM_047416169.1",
"protein_id": "XP_047272125.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 620,
"cds_start": 48,
"cds_end": null,
"cds_length": 1863,
"cdna_start": 380,
"cdna_end": null,
"cdna_length": 3240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "THAP9",
"gene_hgnc_id": 23192,
"hgvs_c": "n.*654G>T",
"hgvs_p": null,
"transcript": "ENST00000505901.1",
"protein_id": "ENSP00000425966.1",
"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": 3348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"hgvs_c": "n.*654G>T",
"hgvs_p": null,
"transcript": "ENST00000505901.1",
"protein_id": "ENSP00000425966.1",
"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": 3348,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LIN54",
"gene_hgnc_id": 25397,
"hgvs_c": "n.305-3668C>A",
"hgvs_p": null,
"transcript": "ENST00000505905.1",
"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": 810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"hgvs_c": "n.*268G>T",
"hgvs_p": null,
"transcript": "ENST00000506208.1",
"protein_id": "ENSP00000424001.1",
"transcript_support_level": 3,
"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": 565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"dbsnp": "rs897945",
"frequency_reference_population": 0.52189714,
"hom_count_reference_population": 231111,
"allele_count_reference_population": 841747,
"gnomad_exomes_af": 0.531497,
"gnomad_genomes_af": 0.429706,
"gnomad_exomes_ac": 776387,
"gnomad_genomes_ac": 65360,
"gnomad_exomes_homalt": 214208,
"gnomad_genomes_homalt": 16903,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.000019059776604990475,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.11,
"revel_prediction": "Benign",
"alphamissense_score": 0.0977,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.354,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000302236.10",
"gene_symbol": "THAP9",
"hgnc_id": 23192,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.897G>T",
"hgvs_p": "p.Leu299Phe"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000505905.1",
"gene_symbol": "LIN54",
"hgnc_id": 25397,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.305-3668C>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}