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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: 14-60648790-TCTC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=60648790&ref=TCTC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 60648790,
"ref": "TCTC",
"alt": "T",
"effect": "conservative_inframe_deletion",
"transcript": "ENST00000645694.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIX1",
"gene_hgnc_id": 10887,
"hgvs_c": "c.397_399delGAG",
"hgvs_p": "p.Glu133del",
"transcript": "NM_005982.4",
"protein_id": "NP_005973.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 284,
"cds_start": 397,
"cds_end": null,
"cds_length": 855,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 4005,
"mane_select": "ENST00000645694.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIX1",
"gene_hgnc_id": 10887,
"hgvs_c": "c.397_399delGAG",
"hgvs_p": "p.Glu133del",
"transcript": "ENST00000645694.3",
"protein_id": "ENSP00000494686.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 284,
"cds_start": 397,
"cds_end": null,
"cds_length": 855,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 4005,
"mane_select": "NM_005982.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIX1",
"gene_hgnc_id": 10887,
"hgvs_c": "c.397_399delGAG",
"hgvs_p": "p.Glu133del",
"transcript": "NM_001425142.1",
"protein_id": "NP_001412071.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 173,
"cds_start": 397,
"cds_end": null,
"cds_length": 522,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 2668,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SIX1",
"gene_hgnc_id": 10887,
"hgvs_c": "c.42-2216_42-2214delGAG",
"hgvs_p": null,
"transcript": "ENST00000554986.2",
"protein_id": "ENSP00000452700.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 111,
"cds_start": -4,
"cds_end": null,
"cds_length": 336,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1959,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SIX1",
"gene_hgnc_id": 10887,
"hgvs_c": "n.249-2216_249-2214delGAG",
"hgvs_p": null,
"transcript": "ENST00000553535.2",
"protein_id": null,
"transcript_support_level": 3,
"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": 1556,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SIX1",
"gene_hgnc_id": 10887,
"hgvs_c": "n.1198-2216_1198-2214delGAG",
"hgvs_p": null,
"transcript": "ENST00000555955.3",
"protein_id": null,
"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": 2844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR9718",
"gene_hgnc_id": 53988,
"hgvs_c": "n.*80_*82delCTC",
"hgvs_p": null,
"transcript": "NR_162089.1",
"protein_id": null,
"transcript_support_level": null,
"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": 64,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR9718",
"gene_hgnc_id": 53988,
"hgvs_c": "n.*91_*93delCTC",
"hgvs_p": null,
"transcript": "unassigned_transcript_2330",
"protein_id": null,
"transcript_support_level": null,
"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": 20,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SIX1",
"gene_hgnc_id": 10887,
"dbsnp": "rs80356460",
"frequency_reference_population": 0.0000013681107,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136811,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"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": 8.012,
"phylop100way_prediction": "Pathogenic",
"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": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM4_Supporting,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 13,
"benign_score": 0,
"pathogenic_score": 13,
"criteria": [
"PM1",
"PM2",
"PM4_Supporting",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000645694.3",
"gene_symbol": "SIX1",
"hgnc_id": 10887,
"effects": [
"conservative_inframe_deletion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.397_399delGAG",
"hgvs_p": "p.Glu133del"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NR_162089.1",
"gene_symbol": "MIR9718",
"hgnc_id": 53988,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*80_*82delCTC",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal dominant nonsyndromic hearing loss 23,Branchiootic syndrome 3,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:5 O:1",
"phenotype_combined": "Autosomal dominant nonsyndromic hearing loss 23|Branchiootic syndrome 3|not provided|Branchiootic syndrome 3;Autosomal dominant nonsyndromic hearing loss 23",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}