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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: 4-82917381-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=82917381&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 82917381,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_024672.6",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"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.1169T>C",
"hgvs_p": "p.Ile390Thr",
"transcript": "NM_024672.6",
"protein_id": "NP_078948.3",
"transcript_support_level": null,
"aa_start": 390,
"aa_end": null,
"aa_length": 903,
"cds_start": 1169,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 1237,
"cdna_end": null,
"cdna_length": 3825,
"mane_select": "ENST00000302236.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024672.6"
},
{
"aa_ref": "I",
"aa_alt": "T",
"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.1169T>C",
"hgvs_p": "p.Ile390Thr",
"transcript": "ENST00000302236.10",
"protein_id": "ENSP00000305533.5",
"transcript_support_level": 1,
"aa_start": 390,
"aa_end": null,
"aa_length": 903,
"cds_start": 1169,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 1237,
"cdna_end": null,
"cdna_length": 3825,
"mane_select": "NM_024672.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000302236.10"
},
{
"aa_ref": "I",
"aa_alt": "T",
"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.737T>C",
"hgvs_p": "p.Ile246Thr",
"transcript": "NM_001317776.2",
"protein_id": "NP_001304705.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 759,
"cds_start": 737,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 1303,
"cdna_end": null,
"cdna_length": 3891,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001317776.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"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.1208T>C",
"hgvs_p": "p.Ile403Thr",
"transcript": "XM_047416165.1",
"protein_id": "XP_047272121.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 916,
"cds_start": 1208,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 3719,
"cdna_end": null,
"cdna_length": 6307,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416165.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"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.737T>C",
"hgvs_p": "p.Ile246Thr",
"transcript": "XM_047416166.1",
"protein_id": "XP_047272122.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 759,
"cds_start": 737,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 2148,
"cdna_end": null,
"cdna_length": 4736,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416166.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"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.737T>C",
"hgvs_p": "p.Ile246Thr",
"transcript": "XM_047416167.1",
"protein_id": "XP_047272123.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 759,
"cds_start": 737,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 1528,
"cdna_end": null,
"cdna_length": 4116,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416167.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"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.737T>C",
"hgvs_p": "p.Ile246Thr",
"transcript": "XM_047416168.1",
"protein_id": "XP_047272124.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 759,
"cds_start": 737,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 982,
"cdna_end": null,
"cdna_length": 3570,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416168.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"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.320T>C",
"hgvs_p": "p.Ile107Thr",
"transcript": "XM_047416169.1",
"protein_id": "XP_047272125.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 620,
"cds_start": 320,
"cds_end": null,
"cds_length": 1863,
"cdna_start": 652,
"cdna_end": null,
"cdna_length": 3240,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416169.1"
},
{
"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.*926T>C",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3348,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000505901.1"
},
{
"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.*926T>C",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3348,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000505901.1"
},
{
"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.305-3940A>G",
"hgvs_p": null,
"transcript": "ENST00000505905.1",
"protein_id": null,
"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": 810,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000505905.1"
}
],
"gene_symbol": "THAP9",
"gene_hgnc_id": 23192,
"dbsnp": "rs1021795745",
"frequency_reference_population": 0.000003718223,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000342114,
"gnomad_genomes_af": 0.00000657151,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.17857405543327332,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.333,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0787,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.014,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_024672.6",
"gene_symbol": "THAP9",
"hgnc_id": 23192,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1169T>C",
"hgvs_p": "p.Ile390Thr"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000505905.1",
"gene_symbol": "LIN54",
"hgnc_id": 25397,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.305-3940A>G",
"hgvs_p": null
}
],
"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
}