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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: 16-69331089-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=69331089&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 69331089,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000306875.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"hgvs_c": "c.1589C>T",
"hgvs_p": "p.Pro530Leu",
"transcript": "NM_032382.5",
"protein_id": "NP_115758.3",
"transcript_support_level": null,
"aa_start": 530,
"aa_end": null,
"aa_length": 612,
"cds_start": 1589,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1601,
"cdna_end": null,
"cdna_length": 4629,
"mane_select": "ENST00000306875.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"hgvs_c": "c.1589C>T",
"hgvs_p": "p.Pro530Leu",
"transcript": "ENST00000306875.10",
"protein_id": "ENSP00000305459.6",
"transcript_support_level": 1,
"aa_start": 530,
"aa_end": null,
"aa_length": 612,
"cds_start": 1589,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1601,
"cdna_end": null,
"cdna_length": 4629,
"mane_select": "NM_032382.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272617",
"gene_hgnc_id": null,
"hgvs_c": "c.352-1910C>T",
"hgvs_p": null,
"transcript": "ENST00000562949.1",
"protein_id": "ENSP00000457718.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 164,
"cds_start": -4,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"hgvs_c": "c.1730C>T",
"hgvs_p": "p.Pro577Leu",
"transcript": "NM_001379261.1",
"protein_id": "NP_001366190.1",
"transcript_support_level": null,
"aa_start": 577,
"aa_end": null,
"aa_length": 659,
"cds_start": 1730,
"cds_end": null,
"cds_length": 1980,
"cdna_start": 1742,
"cdna_end": null,
"cdna_length": 4770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"hgvs_c": "c.1589C>T",
"hgvs_p": "p.Pro530Leu",
"transcript": "NM_001379262.1",
"protein_id": "NP_001366191.1",
"transcript_support_level": null,
"aa_start": 530,
"aa_end": null,
"aa_length": 638,
"cds_start": 1589,
"cds_end": null,
"cds_length": 1917,
"cdna_start": 1601,
"cdna_end": null,
"cdna_length": 4523,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"hgvs_c": "c.1628C>T",
"hgvs_p": "p.Pro543Leu",
"transcript": "NM_001379263.1",
"protein_id": "NP_001366192.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 625,
"cds_start": 1628,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 1640,
"cdna_end": null,
"cdna_length": 4668,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"hgvs_c": "c.1589C>T",
"hgvs_p": "p.Pro530Leu",
"transcript": "NM_001379264.1",
"protein_id": "NP_001366193.1",
"transcript_support_level": null,
"aa_start": 530,
"aa_end": null,
"aa_length": 612,
"cds_start": 1589,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1601,
"cdna_end": null,
"cdna_length": 4626,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"hgvs_c": "c.1582+1625C>T",
"hgvs_p": null,
"transcript": "NM_001379265.1",
"protein_id": "NP_001366194.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 579,
"cds_start": -4,
"cds_end": null,
"cds_length": 1740,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"hgvs_c": "c.1414-1910C>T",
"hgvs_p": null,
"transcript": "NM_001379266.1",
"protein_id": "NP_001366195.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 518,
"cds_start": -4,
"cds_end": null,
"cds_length": 1557,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"hgvs_c": "c.548+4237C>T",
"hgvs_p": null,
"transcript": "ENST00000562595.5",
"protein_id": "ENSP00000456705.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 222,
"cds_start": -4,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"dbsnp": "rs114861924",
"frequency_reference_population": 0.0016159373,
"hom_count_reference_population": 36,
"allele_count_reference_population": 2608,
"gnomad_exomes_af": 0.000871661,
"gnomad_genomes_af": 0.00875638,
"gnomad_exomes_ac": 1274,
"gnomad_genomes_ac": 1334,
"gnomad_exomes_homalt": 14,
"gnomad_genomes_homalt": 22,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005343407392501831,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.125,
"revel_prediction": "Benign",
"alphamissense_score": 0.0931,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.459,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000306875.10",
"gene_symbol": "COG8",
"hgnc_id": 18623,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1589C>T",
"hgvs_p": "p.Pro530Leu"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000562949.1",
"gene_symbol": "ENSG00000272617",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.352-1910C>T",
"hgvs_p": null
}
],
"clinvar_disease": "COG8-congenital disorder of glycosylation,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:5",
"phenotype_combined": "not provided|not specified|COG8-congenital disorder of glycosylation",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}