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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: 10-46462402-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=46462402&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "NPY4R",
"hgnc_id": 9329,
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Leu78Leu",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -7,
"transcript": "NM_005972.6",
"verdict": "Benign"
},
{
"benign_score": 6,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000285402",
"hgnc_id": null,
"hgvs_c": "n.254-14076C>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -6,
"transcript": "ENST00000616785.1",
"verdict": "Likely_benign"
},
{
"benign_score": 6,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LINC00842",
"hgnc_id": 44989,
"hgvs_c": "n.384-14076C>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -6,
"transcript": "ENST00000716468.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_score": -7,
"allele_count_reference_population": 4797,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.64,
"chr": "10",
"clinvar_classification": "Benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6399999856948853,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 375,
"aa_ref": "L",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2033,
"cdna_start": 730,
"cds_end": null,
"cds_length": 1128,
"cds_start": 234,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_005972.6",
"gene_hgnc_id": 9329,
"gene_symbol": "NPY4R",
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Leu78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000374312.5",
"protein_coding": true,
"protein_id": "NP_005963.4",
"strand": false,
"transcript": "NM_005972.6",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 375,
"aa_ref": "L",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2033,
"cdna_start": 730,
"cds_end": null,
"cds_length": 1128,
"cds_start": 234,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000374312.5",
"gene_hgnc_id": 9329,
"gene_symbol": "NPY4R",
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Leu78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005972.6",
"protein_coding": true,
"protein_id": "ENSP00000363431.1",
"strand": false,
"transcript": "ENST00000374312.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 375,
"aa_ref": "L",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1800,
"cdna_start": 497,
"cds_end": null,
"cds_length": 1128,
"cds_start": 234,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000612632.3",
"gene_hgnc_id": 9329,
"gene_symbol": "NPY4R",
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Leu78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000480883.1",
"strand": false,
"transcript": "ENST00000612632.3",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 375,
"aa_ref": "L",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1877,
"cdna_start": 574,
"cds_end": null,
"cds_length": 1128,
"cds_start": 234,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001278794.2",
"gene_hgnc_id": 9329,
"gene_symbol": "NPY4R",
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Leu78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001265723.1",
"strand": false,
"transcript": "NM_001278794.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 375,
"aa_ref": "L",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4066,
"cdna_start": 549,
"cds_end": null,
"cds_length": 1128,
"cds_start": 234,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000908575.1",
"gene_hgnc_id": 9329,
"gene_symbol": "NPY4R",
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Leu78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578634.1",
"strand": false,
"transcript": "ENST00000908575.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 375,
"aa_ref": "L",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5812,
"cdna_start": 1305,
"cds_end": null,
"cds_length": 1128,
"cds_start": 234,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000908576.1",
"gene_hgnc_id": 9329,
"gene_symbol": "NPY4R",
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Leu78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578635.1",
"strand": false,
"transcript": "ENST00000908576.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 375,
"aa_ref": "L",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4892,
"cdna_start": 3589,
"cds_end": null,
"cds_length": 1128,
"cds_start": 234,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_011539936.4",
"gene_hgnc_id": 9329,
"gene_symbol": "NPY4R",
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Leu78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011538238.1",
"strand": false,
"transcript": "XM_011539936.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 375,
"aa_ref": "L",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1930,
"cdna_start": 627,
"cds_end": null,
"cds_length": 1128,
"cds_start": 234,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_011539937.4",
"gene_hgnc_id": 9329,
"gene_symbol": "NPY4R",
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Leu78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011538239.1",
"strand": false,
"transcript": "XM_011539937.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 375,
"aa_ref": "L",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2599,
"cdna_start": 1296,
"cds_end": null,
"cds_length": 1128,
"cds_start": 234,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_017016386.3",
"gene_hgnc_id": 9329,
"gene_symbol": "NPY4R",
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Leu78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016871875.1",
"strand": false,
"transcript": "XM_017016386.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 375,
"aa_ref": "L",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2206,
"cdna_start": 903,
"cds_end": null,
"cds_length": 1128,
"cds_start": 234,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_017016387.3",
"gene_hgnc_id": 9329,
"gene_symbol": "NPY4R",
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Leu78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016871876.1",
"strand": false,
"transcript": "XM_017016387.3",
"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": 1700,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000616785.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285402",
"hgvs_c": "n.254-14076C>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000616785.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 851,
"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": "ENST00000716468.1",
"gene_hgnc_id": 44989,
"gene_symbol": "LINC00842",
"hgvs_c": "n.384-14076C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000716468.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs28691230",
"effect": "synonymous_variant",
"frequency_reference_population": 0.002976124,
"gene_hgnc_id": 9329,
"gene_symbol": "NPY4R",
"gnomad_exomes_ac": 2360,
"gnomad_exomes_af": 0.00161571,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 2437,
"gnomad_genomes_af": 0.0161205,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.501,
"pos": 46462402,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005972.6"
}
]
}