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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: 16-28538022-GC-AT (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=28538022&ref=GC&alt=AT&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "NUPR1",
"hgnc_id": 29990,
"hgvs_c": "c.299_300delGCinsAT",
"hgvs_p": "p.Arg100His",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_001042483.2",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000289754",
"hgnc_id": null,
"hgvs_c": "n.333_334delGCinsAT",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "ENST00000679262.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "AT",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "16",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 82,
"aa_ref": "R",
"aa_start": 82,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5291,
"cdna_start": 313,
"cds_end": null,
"cds_length": 249,
"cds_start": 245,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_012385.3",
"gene_hgnc_id": 29990,
"gene_symbol": "NUPR1",
"hgvs_c": "c.245_246delGCinsAT",
"hgvs_p": "p.Arg82His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000324873.8",
"protein_coding": true,
"protein_id": "NP_036517.1",
"strand": false,
"transcript": "NM_012385.3",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 82,
"aa_ref": "R",
"aa_start": 82,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5291,
"cdna_start": 313,
"cds_end": null,
"cds_length": 249,
"cds_start": 245,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000324873.8",
"gene_hgnc_id": 29990,
"gene_symbol": "NUPR1",
"hgvs_c": "c.245_246delGCinsAT",
"hgvs_p": "p.Arg82His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_012385.3",
"protein_coding": true,
"protein_id": "ENSP00000315559.7",
"strand": false,
"transcript": "ENST00000324873.8",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 109,
"aa_ref": "R",
"aa_start": 109,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 740,
"cdna_start": 395,
"cds_end": null,
"cds_length": 330,
"cds_start": 326,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000876798.1",
"gene_hgnc_id": 29990,
"gene_symbol": "NUPR1",
"hgvs_c": "c.326_327delGCinsAT",
"hgvs_p": "p.Arg109His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546857.1",
"strand": false,
"transcript": "ENST00000876798.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 100,
"aa_ref": "R",
"aa_start": 100,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5345,
"cdna_start": 367,
"cds_end": null,
"cds_length": 303,
"cds_start": 299,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001042483.2",
"gene_hgnc_id": 29990,
"gene_symbol": "NUPR1",
"hgvs_c": "c.299_300delGCinsAT",
"hgvs_p": "p.Arg100His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001035948.1",
"strand": false,
"transcript": "NM_001042483.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 100,
"aa_ref": "R",
"aa_start": 100,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 550,
"cdna_start": 401,
"cds_end": null,
"cds_length": 303,
"cds_start": 299,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000395641.2",
"gene_hgnc_id": 29990,
"gene_symbol": "NUPR1",
"hgvs_c": "c.299_300delGCinsAT",
"hgvs_p": "p.Arg100His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000379003.2",
"strand": false,
"transcript": "ENST00000395641.2",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 82,
"aa_ref": "R",
"aa_start": 82,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 713,
"cdna_start": 377,
"cds_end": null,
"cds_length": 249,
"cds_start": 245,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000962926.1",
"gene_hgnc_id": 29990,
"gene_symbol": "NUPR1",
"hgvs_c": "c.245_246delGCinsAT",
"hgvs_p": "p.Arg82His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632985.1",
"strand": false,
"transcript": "ENST00000962926.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 81,
"aa_ref": "R",
"aa_start": 81,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 623,
"cdna_start": 307,
"cds_end": null,
"cds_length": 246,
"cds_start": 242,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000876799.1",
"gene_hgnc_id": 29990,
"gene_symbol": "NUPR1",
"hgvs_c": "c.242_243delGCinsAT",
"hgvs_p": "p.Arg81His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546858.1",
"strand": false,
"transcript": "ENST00000876799.1",
"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": 598,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000567646.1",
"gene_hgnc_id": 29990,
"gene_symbol": "NUPR1",
"hgvs_c": "n.*242_*243delGCinsAT",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000456597.1",
"strand": false,
"transcript": "ENST00000567646.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 980,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000679262.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000289754",
"hgvs_c": "n.333_334delGCinsAT",
"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": "ENST00000679262.2",
"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": 598,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000567646.1",
"gene_hgnc_id": 29990,
"gene_symbol": "NUPR1",
"hgvs_c": "n.*242_*243delGCinsAT",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000456597.1",
"strand": false,
"transcript": "ENST00000567646.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 29990,
"gene_symbol": "NUPR1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"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": "Benign",
"phylop100way_score": 1.886,
"pos": 28538022,
"ref": "GC",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_001042483.2"
}
]
}