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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: 1-161751718-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=161751718&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DUSP12",
"hgnc_id": 3067,
"hgvs_c": "c.395A>C",
"hgvs_p": "p.Lys132Thr",
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_007240.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ATF6-DT",
"hgnc_id": 55826,
"hgvs_c": "n.373-1351T>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 3,
"score": 3,
"transcript": "ENST00000702792.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_score": 3,
"allele_count_reference_population": 8,
"alphamissense_prediction": "Uncertain_significance",
"alphamissense_score": 0.4672,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.11,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8172762393951416,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 340,
"aa_ref": "K",
"aa_start": 132,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1330,
"cdna_start": 411,
"cds_end": null,
"cds_length": 1023,
"cds_start": 395,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_007240.3",
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"hgvs_c": "c.395A>C",
"hgvs_p": "p.Lys132Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000367943.5",
"protein_coding": true,
"protein_id": "NP_009171.1",
"strand": true,
"transcript": "NM_007240.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 340,
"aa_ref": "K",
"aa_start": 132,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1330,
"cdna_start": 411,
"cds_end": null,
"cds_length": 1023,
"cds_start": 395,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000367943.5",
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"hgvs_c": "c.395A>C",
"hgvs_p": "p.Lys132Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_007240.3",
"protein_coding": true,
"protein_id": "ENSP00000356920.4",
"strand": true,
"transcript": "ENST00000367943.5",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 379,
"aa_ref": "K",
"aa_start": 171,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1364,
"cdna_start": 521,
"cds_end": null,
"cds_length": 1140,
"cds_start": 512,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000931531.1",
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"hgvs_c": "c.512A>C",
"hgvs_p": "p.Lys171Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601590.1",
"strand": true,
"transcript": "ENST00000931531.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 351,
"aa_ref": "K",
"aa_start": 143,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1284,
"cdna_start": 442,
"cds_end": null,
"cds_length": 1056,
"cds_start": 428,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000954828.1",
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"hgvs_c": "c.428A>C",
"hgvs_p": "p.Lys143Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624887.1",
"strand": true,
"transcript": "ENST00000954828.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 321,
"aa_ref": "K",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1202,
"cdna_start": 359,
"cds_end": null,
"cds_length": 966,
"cds_start": 338,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000954827.1",
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"hgvs_c": "c.338A>C",
"hgvs_p": "p.Lys113Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624886.1",
"strand": true,
"transcript": "ENST00000954827.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 210,
"aa_ref": "K",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1343,
"cdna_start": 424,
"cds_end": null,
"cds_length": 633,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_005244862.4",
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"hgvs_c": "c.5A>C",
"hgvs_p": "p.Lys2Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005244919.1",
"strand": true,
"transcript": "XM_005244862.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 302,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1143,
"cdna_start": null,
"cds_end": null,
"cds_length": 909,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000881382.1",
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"hgvs_c": "c.345-148A>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551441.1",
"strand": true,
"transcript": "ENST00000881382.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 740,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000464004.2",
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"hgvs_c": "n.408A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000476912.1",
"strand": true,
"transcript": "ENST00000464004.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1252,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000484291.5",
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"hgvs_c": "n.408A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000476528.1",
"strand": true,
"transcript": "ENST00000484291.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 657,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000490591.1",
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"hgvs_c": "n.*270A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000477122.1",
"strand": true,
"transcript": "ENST00000490591.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 657,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000490591.1",
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"hgvs_c": "n.*270A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000477122.1",
"strand": true,
"transcript": "ENST00000490591.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1288,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000702792.1",
"gene_hgnc_id": 55826,
"gene_symbol": "ATF6-DT",
"hgvs_c": "n.373-1351T>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000702792.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1445724832",
"effect": "missense_variant",
"frequency_reference_population": 0.0000049578334,
"gene_hgnc_id": 3067,
"gene_symbol": "DUSP12",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000273693,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262961,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.824,
"pos": 161751718,
"ref": "A",
"revel_prediction": "Pathogenic",
"revel_score": 0.708,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_007240.3"
}
]
}