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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: 3-23956113-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=23956113&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 23956113,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_005126.5",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "c.360C>T",
"hgvs_p": "p.Cys120Cys",
"transcript": "NM_005126.5",
"protein_id": "NP_005117.3",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 579,
"cds_start": 360,
"cds_end": null,
"cds_length": 1740,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000312521.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005126.5"
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "c.360C>T",
"hgvs_p": "p.Cys120Cys",
"transcript": "ENST00000312521.9",
"protein_id": "ENSP00000310006.3",
"transcript_support_level": 1,
"aa_start": 120,
"aa_end": null,
"aa_length": 579,
"cds_start": 360,
"cds_end": null,
"cds_length": 1740,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005126.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000312521.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "n.360C>T",
"hgvs_p": null,
"transcript": "ENST00000383773.8",
"protein_id": "ENSP00000373283.3",
"transcript_support_level": 1,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000383773.8"
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "c.360C>T",
"hgvs_p": "p.Cys120Cys",
"transcript": "ENST00000947380.1",
"protein_id": "ENSP00000617439.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 517,
"cds_start": 360,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947380.1"
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "c.135C>T",
"hgvs_p": "p.Cys45Cys",
"transcript": "NM_001145425.2",
"protein_id": "NP_001138897.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 504,
"cds_start": 135,
"cds_end": null,
"cds_length": 1515,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145425.2"
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "c.135C>T",
"hgvs_p": "p.Cys45Cys",
"transcript": "ENST00000492552.6",
"protein_id": "ENSP00000520893.1",
"transcript_support_level": 2,
"aa_start": 45,
"aa_end": null,
"aa_length": 504,
"cds_start": 135,
"cds_end": null,
"cds_length": 1515,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000492552.6"
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "c.93C>T",
"hgvs_p": "p.Cys31Cys",
"transcript": "ENST00000873729.1",
"protein_id": "ENSP00000543788.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 490,
"cds_start": 93,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873729.1"
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "c.360C>T",
"hgvs_p": "p.Cys120Cys",
"transcript": "ENST00000873728.1",
"protein_id": "ENSP00000543787.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 321,
"cds_start": 360,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873728.1"
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "c.360C>T",
"hgvs_p": "p.Cys120Cys",
"transcript": "XM_006713451.4",
"protein_id": "XP_006713514.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 448,
"cds_start": 360,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006713451.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "c.283+1310C>T",
"hgvs_p": null,
"transcript": "ENST00000873730.1",
"protein_id": "ENSP00000543789.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 501,
"cds_start": null,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873730.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "n.255C>T",
"hgvs_p": null,
"transcript": "ENST00000468700.1",
"protein_id": null,
"transcript_support_level": 3,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000468700.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"hgvs_c": "n.653C>T",
"hgvs_p": null,
"transcript": "NR_110524.2",
"protein_id": null,
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_110524.2"
}
],
"gene_symbol": "NR1D2",
"gene_hgnc_id": 7963,
"dbsnp": "rs61732085",
"frequency_reference_population": 0.0053332075,
"hom_count_reference_population": 399,
"allele_count_reference_population": 8600,
"gnomad_exomes_af": 0.00306426,
"gnomad_genomes_af": 0.0271107,
"gnomad_exomes_ac": 4475,
"gnomad_genomes_ac": 4125,
"gnomad_exomes_homalt": 188,
"gnomad_genomes_homalt": 211,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.36000001430511475,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.429,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_005126.5",
"gene_symbol": "NR1D2",
"hgnc_id": 7963,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.360C>T",
"hgvs_p": "p.Cys120Cys"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}