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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: 5-149907345-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=149907345&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 149907345,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000255266.10",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.1032C>A",
"hgvs_p": "p.Ser344Arg",
"transcript": "NM_000440.3",
"protein_id": "NP_000431.2",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 860,
"cds_start": 1032,
"cds_end": null,
"cds_length": 2583,
"cdna_start": 1152,
"cdna_end": null,
"cdna_length": 5645,
"mane_select": "ENST00000255266.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.1032C>A",
"hgvs_p": "p.Ser344Arg",
"transcript": "ENST00000255266.10",
"protein_id": "ENSP00000255266.5",
"transcript_support_level": 1,
"aa_start": 344,
"aa_end": null,
"aa_length": 860,
"cds_start": 1032,
"cds_end": null,
"cds_length": 2583,
"cdna_start": 1152,
"cdna_end": null,
"cdna_length": 5645,
"mane_select": "NM_000440.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "n.1152C>A",
"hgvs_p": null,
"transcript": "ENST00000508173.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 5706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.789C>A",
"hgvs_p": "p.Ser263Arg",
"transcript": "NM_001410788.1",
"protein_id": "NP_001397717.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 779,
"cds_start": 789,
"cds_end": null,
"cds_length": 2340,
"cdna_start": 909,
"cdna_end": null,
"cdna_length": 5402,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.789C>A",
"hgvs_p": "p.Ser263Arg",
"transcript": "ENST00000613228.1",
"protein_id": "ENSP00000478060.1",
"transcript_support_level": 5,
"aa_start": 263,
"aa_end": null,
"aa_length": 779,
"cds_start": 789,
"cds_end": null,
"cds_length": 2340,
"cdna_start": 909,
"cdna_end": null,
"cdna_length": 5398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.147C>A",
"hgvs_p": "p.Ser49Arg",
"transcript": "XM_011537650.3",
"protein_id": "XP_011535952.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 565,
"cds_start": 147,
"cds_end": null,
"cds_length": 1698,
"cdna_start": 285,
"cdna_end": null,
"cdna_length": 3903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"dbsnp": "rs121918577",
"frequency_reference_population": 0.000002052534,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205253,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9324358701705933,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.5,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9945,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": -0.435,
"phylop100way_prediction": "Benign",
"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": "ENST00000255266.10",
"gene_symbol": "PDE6A",
"hgnc_id": 8785,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1032C>A",
"hgvs_p": "p.Ser344Arg"
}
],
"clinvar_disease": "Retinitis pigmentosa 43",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Retinitis pigmentosa 43",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}