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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: 10-12898507-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=12898507&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 12898507,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_031455.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC3",
"gene_hgnc_id": 23813,
"hgvs_c": "c.722C>G",
"hgvs_p": "p.Ala241Gly",
"transcript": "NM_031455.4",
"protein_id": "NP_113643.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 270,
"cds_start": 722,
"cds_end": null,
"cds_length": 813,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000378825.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_031455.4"
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC3",
"gene_hgnc_id": 23813,
"hgvs_c": "c.722C>G",
"hgvs_p": "p.Ala241Gly",
"transcript": "ENST00000378825.5",
"protein_id": "ENSP00000368102.3",
"transcript_support_level": 1,
"aa_start": 241,
"aa_end": null,
"aa_length": 270,
"cds_start": 722,
"cds_end": null,
"cds_length": 813,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_031455.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378825.5"
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC3",
"gene_hgnc_id": 23813,
"hgvs_c": "c.701C>G",
"hgvs_p": "p.Ala234Gly",
"transcript": "ENST00000870347.1",
"protein_id": "ENSP00000540406.1",
"transcript_support_level": null,
"aa_start": 234,
"aa_end": null,
"aa_length": 263,
"cds_start": 701,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870347.1"
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC3",
"gene_hgnc_id": 23813,
"hgvs_c": "c.347C>G",
"hgvs_p": "p.Ala116Gly",
"transcript": "NM_001282658.2",
"protein_id": "NP_001269587.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 145,
"cds_start": 347,
"cds_end": null,
"cds_length": 438,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001282658.2"
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC3",
"gene_hgnc_id": 23813,
"hgvs_c": "c.347C>G",
"hgvs_p": "p.Ala116Gly",
"transcript": "ENST00000378839.1",
"protein_id": "ENSP00000368116.1",
"transcript_support_level": 2,
"aa_start": 116,
"aa_end": null,
"aa_length": 145,
"cds_start": 347,
"cds_end": null,
"cds_length": 438,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378839.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285520",
"gene_hgnc_id": null,
"hgvs_c": "n.511-5G>C",
"hgvs_p": null,
"transcript": "ENST00000649832.1",
"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": "ENST00000649832.1"
}
],
"gene_symbol": "CCDC3",
"gene_hgnc_id": 23813,
"dbsnp": "rs140936699",
"frequency_reference_population": 6.8410685e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84107e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.052654266357421875,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.031,
"revel_prediction": "Benign",
"alphamissense_score": 0.1137,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.232,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_031455.4",
"gene_symbol": "CCDC3",
"hgnc_id": 23813,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.722C>G",
"hgvs_p": "p.Ala241Gly"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000649832.1",
"gene_symbol": "ENSG00000285520",
"hgnc_id": null,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.511-5G>C",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}