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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: 2-241602982-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=241602982&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "THAP4",
"hgnc_id": 23187,
"hgvs_c": "c.1498G>A",
"hgvs_p": "p.Ala500Thr",
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_015963.6",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_score": 3,
"allele_count_reference_population": 13,
"alphamissense_prediction": null,
"alphamissense_score": 0.4708,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.44,
"chr": "2",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8331656455993652,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 577,
"aa_ref": "A",
"aa_start": 500,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2076,
"cdna_start": 1639,
"cds_end": null,
"cds_length": 1734,
"cds_start": 1498,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_015963.6",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.1498G>A",
"hgvs_p": "p.Ala500Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000407315.6",
"protein_coding": true,
"protein_id": "NP_057047.4",
"strand": false,
"transcript": "NM_015963.6",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 577,
"aa_ref": "A",
"aa_start": 500,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2076,
"cdna_start": 1639,
"cds_end": null,
"cds_length": 1734,
"cds_start": 1498,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000407315.6",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.1498G>A",
"hgvs_p": "p.Ala500Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015963.6",
"protein_coding": true,
"protein_id": "ENSP00000385006.1",
"strand": false,
"transcript": "ENST00000407315.6",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 165,
"aa_ref": "A",
"aa_start": 88,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 785,
"cdna_start": 348,
"cds_end": null,
"cds_length": 498,
"cds_start": 262,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000402136.5",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.262G>A",
"hgvs_p": "p.Ala88Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000385931.1",
"strand": false,
"transcript": "ENST00000402136.5",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 605,
"aa_ref": "A",
"aa_start": 500,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2152,
"cdna_start": 1631,
"cds_end": null,
"cds_length": 1818,
"cds_start": 1498,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000863246.1",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.1498G>A",
"hgvs_p": "p.Ala500Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533305.1",
"strand": false,
"transcript": "ENST00000863246.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 604,
"aa_ref": "A",
"aa_start": 500,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2190,
"cdna_start": 1672,
"cds_end": null,
"cds_length": 1815,
"cds_start": 1498,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000863245.1",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.1498G>A",
"hgvs_p": "p.Ala500Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533304.1",
"strand": false,
"transcript": "ENST00000863245.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 591,
"aa_ref": "A",
"aa_start": 500,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2074,
"cdna_start": 1618,
"cds_end": null,
"cds_length": 1776,
"cds_start": 1498,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000863247.1",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.1498G>A",
"hgvs_p": "p.Ala500Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533306.1",
"strand": false,
"transcript": "ENST00000863247.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 546,
"aa_ref": "A",
"aa_start": 469,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1840,
"cdna_start": 1428,
"cds_end": null,
"cds_length": 1641,
"cds_start": 1405,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000863248.1",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.1405G>A",
"hgvs_p": "p.Ala469Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533307.1",
"strand": false,
"transcript": "ENST00000863248.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 192,
"aa_ref": "A",
"aa_start": 88,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 833,
"cdna_start": 337,
"cds_end": null,
"cds_length": 579,
"cds_start": 262,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000402545.5",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.262G>A",
"hgvs_p": "p.Ala88Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000384352.1",
"strand": false,
"transcript": "ENST00000402545.5",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 165,
"aa_ref": "A",
"aa_start": 88,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 776,
"cdna_start": 339,
"cds_end": null,
"cds_length": 498,
"cds_start": 262,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001164356.2",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.262G>A",
"hgvs_p": "p.Ala88Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001157828.1",
"strand": false,
"transcript": "NM_001164356.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 628,
"aa_ref": "A",
"aa_start": 524,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2154,
"cdna_start": 1636,
"cds_end": null,
"cds_length": 1887,
"cds_start": 1570,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011511291.3",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.1570G>A",
"hgvs_p": "p.Ala524Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011509593.1",
"strand": false,
"transcript": "XM_011511291.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 604,
"aa_ref": "A",
"aa_start": 500,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2157,
"cdna_start": 1639,
"cds_end": null,
"cds_length": 1815,
"cds_start": 1498,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_005247016.5",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.1498G>A",
"hgvs_p": "p.Ala500Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005247073.4",
"strand": false,
"transcript": "XM_005247016.5",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 601,
"aa_ref": "A",
"aa_start": 524,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2073,
"cdna_start": 1636,
"cds_end": null,
"cds_length": 1806,
"cds_start": 1570,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017004256.2",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "c.1570G>A",
"hgvs_p": "p.Ala524Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016859745.1",
"strand": false,
"transcript": "XM_017004256.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 567,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000497486.1",
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"hgvs_c": "n.13G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000497486.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs756590530",
"effect": "missense_variant",
"frequency_reference_population": 0.000008896432,
"gene_hgnc_id": 23187,
"gene_symbol": "THAP4",
"gnomad_exomes_ac": 13,
"gnomad_exomes_af": 0.00000889643,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.69,
"pos": 241602982,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.703,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_015963.6"
}
]
}