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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: X-21882486-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=21882486&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 21882486,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_015884.4",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBTPS2",
"gene_hgnc_id": 15455,
"hgvs_c": "c.1391T>C",
"hgvs_p": "p.Phe464Ser",
"transcript": "NM_015884.4",
"protein_id": "NP_056968.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 519,
"cds_start": 1391,
"cds_end": null,
"cds_length": 1560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000379484.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015884.4"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBTPS2",
"gene_hgnc_id": 15455,
"hgvs_c": "c.1391T>C",
"hgvs_p": "p.Phe464Ser",
"transcript": "ENST00000379484.10",
"protein_id": "ENSP00000368798.5",
"transcript_support_level": 1,
"aa_start": 464,
"aa_end": null,
"aa_length": 519,
"cds_start": 1391,
"cds_end": null,
"cds_length": 1560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015884.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379484.10"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBTPS2",
"gene_hgnc_id": 15455,
"hgvs_c": "c.1475T>C",
"hgvs_p": "p.Phe492Ser",
"transcript": "ENST00000860794.1",
"protein_id": "ENSP00000530853.1",
"transcript_support_level": null,
"aa_start": 492,
"aa_end": null,
"aa_length": 547,
"cds_start": 1475,
"cds_end": null,
"cds_length": 1644,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860794.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBTPS2",
"gene_hgnc_id": 15455,
"hgvs_c": "c.1295T>C",
"hgvs_p": "p.Phe432Ser",
"transcript": "ENST00000934337.1",
"protein_id": "ENSP00000604396.1",
"transcript_support_level": null,
"aa_start": 432,
"aa_end": null,
"aa_length": 487,
"cds_start": 1295,
"cds_end": null,
"cds_length": 1464,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934337.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBTPS2",
"gene_hgnc_id": 15455,
"hgvs_c": "c.1100T>C",
"hgvs_p": "p.Phe367Ser",
"transcript": "ENST00000860795.1",
"protein_id": "ENSP00000530854.1",
"transcript_support_level": null,
"aa_start": 367,
"aa_end": null,
"aa_length": 422,
"cds_start": 1100,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860795.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBTPS2",
"gene_hgnc_id": 15455,
"hgvs_c": "c.1091T>C",
"hgvs_p": "p.Phe364Ser",
"transcript": "ENST00000860793.1",
"protein_id": "ENSP00000530852.1",
"transcript_support_level": null,
"aa_start": 364,
"aa_end": null,
"aa_length": 419,
"cds_start": 1091,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860793.1"
}
],
"gene_symbol": "MBTPS2",
"gene_hgnc_id": 15455,
"dbsnp": "rs587777306",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9386032819747925,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.85,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9976,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.563,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.05,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_015884.4",
"gene_symbol": "MBTPS2",
"hgnc_id": 15455,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,XL",
"hgvs_c": "c.1391T>C",
"hgvs_p": "p.Phe464Ser"
}
],
"clinvar_disease": " X-linked,Olmsted syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Olmsted syndrome, X-linked",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}