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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: 5-116001165-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=116001165&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 116001165,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000357872.9",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "c.1746T>C",
"hgvs_p": "p.Asn582Asn",
"transcript": "NM_173800.5",
"protein_id": "NP_776161.3",
"transcript_support_level": null,
"aa_start": 582,
"aa_end": null,
"aa_length": 990,
"cds_start": 1746,
"cds_end": null,
"cds_length": 2973,
"cdna_start": 1889,
"cdna_end": null,
"cdna_length": 4604,
"mane_select": "ENST00000357872.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "c.1746T>C",
"hgvs_p": "p.Asn582Asn",
"transcript": "ENST00000357872.9",
"protein_id": "ENSP00000350541.4",
"transcript_support_level": 1,
"aa_start": 582,
"aa_end": null,
"aa_length": 990,
"cds_start": 1746,
"cds_end": null,
"cds_length": 2973,
"cdna_start": 1889,
"cdna_end": null,
"cdna_length": 4604,
"mane_select": "NM_173800.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "n.1746T>C",
"hgvs_p": null,
"transcript": "ENST00000504467.5",
"protein_id": "ENSP00000423604.1",
"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": 3322,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "c.1053T>C",
"hgvs_p": "p.Asn351Asn",
"transcript": "XM_047416913.1",
"protein_id": "XP_047272869.1",
"transcript_support_level": null,
"aa_start": 351,
"aa_end": null,
"aa_length": 759,
"cds_start": 1053,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 1073,
"cdna_end": null,
"cdna_length": 3788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "c.957T>C",
"hgvs_p": "p.Asn319Asn",
"transcript": "XM_047416914.1",
"protein_id": "XP_047272870.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 727,
"cds_start": 957,
"cds_end": null,
"cds_length": 2184,
"cdna_start": 3440,
"cdna_end": null,
"cdna_length": 6155,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "c.957T>C",
"hgvs_p": "p.Asn319Asn",
"transcript": "XM_047416915.1",
"protein_id": "XP_047272871.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 727,
"cds_start": 957,
"cds_end": null,
"cds_length": 2184,
"cdna_start": 1071,
"cdna_end": null,
"cdna_length": 3786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "c.522T>C",
"hgvs_p": "p.Asn174Asn",
"transcript": "XM_047416916.1",
"protein_id": "XP_047272872.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 582,
"cds_start": 522,
"cds_end": null,
"cds_length": 1749,
"cdna_start": 620,
"cdna_end": null,
"cdna_length": 3335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Asn125Asn",
"transcript": "XM_047416917.1",
"protein_id": "XP_047272873.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 533,
"cds_start": 375,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 560,
"cdna_end": null,
"cdna_length": 3275,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "c.297T>C",
"hgvs_p": "p.Asn99Asn",
"transcript": "XM_047416918.1",
"protein_id": "XP_047272874.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 507,
"cds_start": 297,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1203,
"cdna_end": null,
"cdna_length": 3918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "c.297T>C",
"hgvs_p": "p.Asn99Asn",
"transcript": "XM_047416919.1",
"protein_id": "XP_047272875.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 507,
"cds_start": 297,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 416,
"cdna_end": null,
"cdna_length": 3131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "n.297T>C",
"hgvs_p": null,
"transcript": "ENST00000503329.5",
"protein_id": "ENSP00000427418.1",
"transcript_support_level": 2,
"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": 3676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "n.297T>C",
"hgvs_p": null,
"transcript": "ENST00000512314.5",
"protein_id": "ENSP00000427500.1",
"transcript_support_level": 2,
"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": 2067,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"hgvs_c": "n.297T>C",
"hgvs_p": null,
"transcript": "ENST00000514509.5",
"protein_id": "ENSP00000427574.1",
"transcript_support_level": 2,
"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": 2354,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LVRN",
"gene_hgnc_id": 26904,
"dbsnp": "rs7712021",
"frequency_reference_population": 0.32022825,
"hom_count_reference_population": 85042,
"allele_count_reference_population": 516646,
"gnomad_exomes_af": 0.320164,
"gnomad_genomes_af": 0.320851,
"gnomad_exomes_ac": 467878,
"gnomad_genomes_ac": 48768,
"gnomad_exomes_homalt": 77044,
"gnomad_genomes_homalt": 7998,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5299999713897705,
"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": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.734,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000357872.9",
"gene_symbol": "LVRN",
"hgnc_id": 26904,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1746T>C",
"hgvs_p": "p.Asn582Asn"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}