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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: 11-89227816-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=89227816&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 89227816,
"ref": "T",
"alt": "A",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000263321.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"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": "TYR",
"gene_hgnc_id": 12442,
"hgvs_c": "c.1037-7T>A",
"hgvs_p": null,
"transcript": "NM_000372.5",
"protein_id": "NP_000363.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 529,
"cds_start": -4,
"cds_end": null,
"cds_length": 1590,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2062,
"mane_select": "ENST00000263321.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"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": "TYR",
"gene_hgnc_id": 12442,
"hgvs_c": "c.1037-7T>A",
"hgvs_p": null,
"transcript": "ENST00000263321.6",
"protein_id": "ENSP00000263321.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 529,
"cds_start": -4,
"cds_end": null,
"cds_length": 1590,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2062,
"mane_select": "NM_000372.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TYR",
"gene_hgnc_id": 12442,
"hgvs_c": "c.1037-7T>A",
"hgvs_p": null,
"transcript": "XM_011542970.3",
"protein_id": "XP_011541272.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 471,
"cds_start": -4,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TYR",
"gene_hgnc_id": 12442,
"dbsnp": "rs61754381",
"frequency_reference_population": 0.0005044025,
"hom_count_reference_population": 3,
"allele_count_reference_population": 813,
"gnomad_exomes_af": 0.000504965,
"gnomad_genomes_af": 0.000499009,
"gnomad_exomes_ac": 737,
"gnomad_genomes_ac": 76,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8100000023841858,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.984000027179718,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.81,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.5,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.95,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.99825608138479,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP3,PP5_Very_Strong,BS2_Supporting",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 1,
"pathogenic_score": 9,
"criteria": [
"PP3",
"PP5_Very_Strong",
"BS2_Supporting"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000263321.6",
"gene_symbol": "TYR",
"hgnc_id": 12442,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1037-7T>A",
"hgvs_p": null
}
],
"clinvar_disease": " LIGHT/DARK SKIN,Abnormality of the skin,Albinism,Albinism or congenital nystagmus,Inborn genetic diseases,Myopia,Nonsyndromic Oculocutaneous Albinism,Nystagmus,Oculocutaneous albinism,Oculocutaneous albinism type 1A,Oculocutaneous albinism type 1B,SKIN/HAIR/EYE PIGMENTATION 3,See cases,TYR-related disorder,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:27 LP:3 O:1",
"phenotype_combined": "not provided|Oculocutaneous albinism type 1A|Oculocutaneous albinism|Myopia;Albinism;Nystagmus|Nonsyndromic Oculocutaneous Albinism|Oculocutaneous albinism type 1B|SKIN/HAIR/EYE PIGMENTATION 3, LIGHT/DARK SKIN;Oculocutaneous albinism type 1A;Oculocutaneous albinism type 1B|SKIN/HAIR/EYE PIGMENTATION 3, LIGHT/DARK SKIN|TYR-related disorder|Abnormality of the skin|Oculocutaneous albinism type 1A;Oculocutaneous albinism type 1B|See cases|Albinism or congenital nystagmus|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}