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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: 9-129814061-TCTC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=129814061&ref=TCTC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 129814061,
"ref": "TCTC",
"alt": "T",
"effect": "conservative_inframe_deletion",
"transcript": "NM_000113.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1A",
"gene_hgnc_id": 3098,
"hgvs_c": "c.907_909delGAG",
"hgvs_p": "p.Glu303del",
"transcript": "NM_000113.3",
"protein_id": "NP_000104.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 332,
"cds_start": 907,
"cds_end": null,
"cds_length": 999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000351698.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000113.3"
},
{
"aa_ref": "E",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1A",
"gene_hgnc_id": 3098,
"hgvs_c": "c.907_909delGAG",
"hgvs_p": "p.Glu303del",
"transcript": "ENST00000351698.5",
"protein_id": "ENSP00000345719.4",
"transcript_support_level": 1,
"aa_start": 303,
"aa_end": null,
"aa_length": 332,
"cds_start": 907,
"cds_end": null,
"cds_length": 999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000113.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000351698.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1A",
"gene_hgnc_id": 3098,
"hgvs_c": "c.*175_*177delGAG",
"hgvs_p": null,
"transcript": "ENST00000651202.1",
"protein_id": "ENSP00000498222.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 315,
"cds_start": null,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000651202.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1A",
"gene_hgnc_id": 3098,
"hgvs_c": "n.491_493delGAG",
"hgvs_p": null,
"transcript": "ENST00000474192.1",
"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": "pseudogene",
"feature": "ENST00000474192.1"
}
],
"gene_symbol": "TOR1A",
"gene_hgnc_id": 3098,
"dbsnp": "rs80358233",
"frequency_reference_population": 0.000052039064,
"hom_count_reference_population": 0,
"allele_count_reference_population": 84,
"gnomad_exomes_af": 0.0000519874,
"gnomad_genomes_af": 0.0000525348,
"gnomad_exomes_ac": 76,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"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": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 4.736,
"phylop100way_prediction": "Uncertain_significance",
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM4_Supporting,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM4_Supporting",
"PP5_Very_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000113.3",
"gene_symbol": "TOR1A",
"hgnc_id": 3098,
"effects": [
"conservative_inframe_deletion"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.907_909delGAG",
"hgvs_p": "p.Glu303del"
}
],
"clinvar_disease": "Arthrogryposis multiplex congenita 5,Dystonic disorder,Early-onset generalized limb-onset dystonia,Inborn genetic diseases,TOR1A-related disorder,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:18 LP:1 O:1",
"phenotype_combined": "Early-onset generalized limb-onset dystonia|not provided|Dystonic disorder|Early-onset generalized limb-onset dystonia;Arthrogryposis multiplex congenita 5|TOR1A-related disorder|Arthrogryposis multiplex congenita 5|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}