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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: 17-28552493-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=28552493&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 28552493,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000335765.9",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UNC119",
"gene_hgnc_id": 12565,
"hgvs_c": "c.65G>T",
"hgvs_p": "p.Gly22Val",
"transcript": "NM_005148.4",
"protein_id": "NP_005139.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 240,
"cds_start": 65,
"cds_end": null,
"cds_length": 723,
"cdna_start": 132,
"cdna_end": null,
"cdna_length": 1379,
"mane_select": "ENST00000335765.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UNC119",
"gene_hgnc_id": 12565,
"hgvs_c": "c.65G>T",
"hgvs_p": "p.Gly22Val",
"transcript": "ENST00000335765.9",
"protein_id": "ENSP00000337040.3",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 240,
"cds_start": 65,
"cds_end": null,
"cds_length": 723,
"cdna_start": 132,
"cdna_end": null,
"cdna_length": 1379,
"mane_select": "NM_005148.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UNC119",
"gene_hgnc_id": 12565,
"hgvs_c": "c.65G>T",
"hgvs_p": "p.Gly22Val",
"transcript": "ENST00000301032.8",
"protein_id": "ENSP00000301032.4",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 220,
"cds_start": 65,
"cds_end": null,
"cds_length": 663,
"cdna_start": 139,
"cdna_end": null,
"cdna_length": 1653,
"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": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "RSKR",
"gene_hgnc_id": 26314,
"hgvs_c": "n.*1195+51558G>T",
"hgvs_p": null,
"transcript": "ENST00000481916.6",
"protein_id": "ENSP00000436369.2",
"transcript_support_level": 1,
"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": 2091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UNC119",
"gene_hgnc_id": 12565,
"hgvs_c": "c.65G>T",
"hgvs_p": "p.Gly22Val",
"transcript": "NM_054035.2",
"protein_id": "NP_473376.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 220,
"cds_start": 65,
"cds_end": null,
"cds_length": 663,
"cdna_start": 136,
"cdna_end": null,
"cdna_length": 1651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UNC119",
"gene_hgnc_id": 12565,
"hgvs_c": "c.65G>T",
"hgvs_p": "p.Gly22Val",
"transcript": "ENST00000444148.1",
"protein_id": "ENSP00000414639.1",
"transcript_support_level": 5,
"aa_start": 22,
"aa_end": null,
"aa_length": 207,
"cds_start": 65,
"cds_end": null,
"cds_length": 624,
"cdna_start": 117,
"cdna_end": null,
"cdna_length": 676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UNC119",
"gene_hgnc_id": 12565,
"hgvs_c": "c.56G>T",
"hgvs_p": "p.Gly19Val",
"transcript": "ENST00000581945.1",
"protein_id": "ENSP00000463893.1",
"transcript_support_level": 3,
"aa_start": 19,
"aa_end": null,
"aa_length": 85,
"cds_start": 56,
"cds_end": null,
"cds_length": 258,
"cdna_start": 57,
"cdna_end": null,
"cdna_length": 538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UNC119",
"gene_hgnc_id": 12565,
"hgvs_c": "c.65G>T",
"hgvs_p": "p.Gly22Val",
"transcript": "XM_011525459.3",
"protein_id": "XP_011523761.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 126,
"cds_start": 65,
"cds_end": null,
"cds_length": 381,
"cdna_start": 136,
"cdna_end": null,
"cdna_length": 1548,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UNC119",
"gene_hgnc_id": 12565,
"hgvs_c": "n.133G>T",
"hgvs_p": null,
"transcript": "ENST00000578434.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 556,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UNC119",
"gene_hgnc_id": 12565,
"hgvs_c": "c.-249G>T",
"hgvs_p": null,
"transcript": "NM_001330166.2",
"protein_id": "NP_001317095.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 145,
"cds_start": -4,
"cds_end": null,
"cds_length": 438,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "UNC119",
"gene_hgnc_id": 12565,
"dbsnp": "rs199714731",
"frequency_reference_population": 0.0011768872,
"hom_count_reference_population": 17,
"allele_count_reference_population": 1848,
"gnomad_exomes_af": 0.000618478,
"gnomad_genomes_af": 0.00637775,
"gnomad_exomes_ac": 877,
"gnomad_genomes_ac": 971,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 12,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0030156970024108887,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.135,
"revel_prediction": "Benign",
"alphamissense_score": 0.0736,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.532,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000335765.9",
"gene_symbol": "UNC119",
"hgnc_id": 12565,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.65G>T",
"hgvs_p": "p.Gly22Val"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000481916.6",
"gene_symbol": "RSKR",
"hgnc_id": 26314,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*1195+51558G>T",
"hgvs_p": null
}
],
"clinvar_disease": "Cone-rod dystrophy,Idiopathic CD4 lymphocytopenia,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:3",
"phenotype_combined": "Idiopathic CD4 lymphocytopenia|Cone-rod dystrophy|not specified|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}