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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: 11-89284853-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=89284853&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 89284853,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000372.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYR",
"gene_hgnc_id": 12442,
"hgvs_c": "c.1265G>A",
"hgvs_p": "p.Arg422Gln",
"transcript": "NM_000372.5",
"protein_id": "NP_000363.1",
"transcript_support_level": null,
"aa_start": 422,
"aa_end": null,
"aa_length": 529,
"cds_start": 1265,
"cds_end": null,
"cds_length": 1590,
"cdna_start": 1344,
"cdna_end": null,
"cdna_length": 2062,
"mane_select": "ENST00000263321.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYR",
"gene_hgnc_id": 12442,
"hgvs_c": "c.1265G>A",
"hgvs_p": "p.Arg422Gln",
"transcript": "ENST00000263321.6",
"protein_id": "ENSP00000263321.4",
"transcript_support_level": 1,
"aa_start": 422,
"aa_end": null,
"aa_length": 529,
"cds_start": 1265,
"cds_end": null,
"cds_length": 1590,
"cdna_start": 1344,
"cdna_end": null,
"cdna_length": 2062,
"mane_select": "NM_000372.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYR",
"gene_hgnc_id": 12442,
"hgvs_c": "c.1265G>A",
"hgvs_p": "p.Arg422Gln",
"transcript": "XM_011542970.3",
"protein_id": "XP_011541272.1",
"transcript_support_level": null,
"aa_start": 422,
"aa_end": null,
"aa_length": 471,
"cds_start": 1265,
"cds_end": null,
"cds_length": 1416,
"cdna_start": 1344,
"cdna_end": null,
"cdna_length": 2156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYR",
"gene_hgnc_id": 12442,
"hgvs_c": "n.263G>A",
"hgvs_p": null,
"transcript": "ENST00000528243.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 530,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TYR",
"gene_hgnc_id": 12442,
"dbsnp": "rs61754393",
"frequency_reference_population": 0.000036603084,
"hom_count_reference_population": 0,
"allele_count_reference_population": 59,
"gnomad_exomes_af": 0.0000383565,
"gnomad_genomes_af": 0.0000197501,
"gnomad_exomes_ac": 56,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8334745168685913,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.689,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1049,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.48,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.514,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM5,PP2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM1",
"PM5",
"PP2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000372.5",
"gene_symbol": "TYR",
"hgnc_id": 12442,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1265G>A",
"hgvs_p": "p.Arg422Gln"
}
],
"clinvar_disease": " LIGHT/DARK SKIN,Oculocutaneous albinism type 1A,Oculocutaneous albinism type 1B,SKIN/HAIR/EYE PIGMENTATION 3,TYR-related disorder,Temperature-sensitive oculocutaneous albinism type 1,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6 O:1",
"phenotype_combined": "Temperature-sensitive oculocutaneous albinism type 1|not provided|Oculocutaneous albinism type 1B|SKIN/HAIR/EYE PIGMENTATION 3, LIGHT/DARK SKIN|Oculocutaneous albinism type 1A|TYR-related disorder|Oculocutaneous albinism type 1B;Oculocutaneous albinism type 1A",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}