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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: 5-149884549-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=149884549&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 149884549,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000255266.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.1957C>T",
"hgvs_p": "p.Arg653*",
"transcript": "NM_000440.3",
"protein_id": "NP_000431.2",
"transcript_support_level": null,
"aa_start": 653,
"aa_end": null,
"aa_length": 860,
"cds_start": 1957,
"cds_end": null,
"cds_length": 2583,
"cdna_start": 2077,
"cdna_end": null,
"cdna_length": 5645,
"mane_select": "ENST00000255266.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.1957C>T",
"hgvs_p": "p.Arg653*",
"transcript": "ENST00000255266.10",
"protein_id": "ENSP00000255266.5",
"transcript_support_level": 1,
"aa_start": 653,
"aa_end": null,
"aa_length": 860,
"cds_start": 1957,
"cds_end": null,
"cds_length": 2583,
"cdna_start": 2077,
"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": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "n.2141C>T",
"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": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.1714C>T",
"hgvs_p": "p.Arg572*",
"transcript": "NM_001410788.1",
"protein_id": "NP_001397717.1",
"transcript_support_level": null,
"aa_start": 572,
"aa_end": null,
"aa_length": 779,
"cds_start": 1714,
"cds_end": null,
"cds_length": 2340,
"cdna_start": 1834,
"cdna_end": null,
"cdna_length": 5402,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.1714C>T",
"hgvs_p": "p.Arg572*",
"transcript": "ENST00000613228.1",
"protein_id": "ENSP00000478060.1",
"transcript_support_level": 5,
"aa_start": 572,
"aa_end": null,
"aa_length": 779,
"cds_start": 1714,
"cds_end": null,
"cds_length": 2340,
"cdna_start": 1834,
"cdna_end": null,
"cdna_length": 5398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.1072C>T",
"hgvs_p": "p.Arg358*",
"transcript": "XM_011537650.3",
"protein_id": "XP_011535952.1",
"transcript_support_level": null,
"aa_start": 358,
"aa_end": null,
"aa_length": 565,
"cds_start": 1072,
"cds_end": null,
"cds_length": 1698,
"cdna_start": 1210,
"cdna_end": null,
"cdna_length": 3903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.910C>T",
"hgvs_p": "p.Arg304*",
"transcript": "XM_011537651.2",
"protein_id": "XP_011535953.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 511,
"cds_start": 910,
"cds_end": null,
"cds_length": 1536,
"cdna_start": 1676,
"cdna_end": null,
"cdna_length": 4369,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.880C>T",
"hgvs_p": "p.Arg294*",
"transcript": "XM_011537653.2",
"protein_id": "XP_011535955.1",
"transcript_support_level": null,
"aa_start": 294,
"aa_end": null,
"aa_length": 501,
"cds_start": 880,
"cds_end": null,
"cds_length": 1506,
"cdna_start": 1842,
"cdna_end": null,
"cdna_length": 4535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"hgvs_c": "c.880C>T",
"hgvs_p": "p.Arg294*",
"transcript": "XM_011537654.2",
"protein_id": "XP_011535956.1",
"transcript_support_level": null,
"aa_start": 294,
"aa_end": null,
"aa_length": 501,
"cds_start": 880,
"cds_end": null,
"cds_length": 1506,
"cdna_start": 1839,
"cdna_end": null,
"cdna_length": 4532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDE6A",
"gene_hgnc_id": 8785,
"dbsnp": "rs753942596",
"frequency_reference_population": 0.000017972414,
"hom_count_reference_population": 0,
"allele_count_reference_population": 29,
"gnomad_exomes_af": 0.0000184728,
"gnomad_genomes_af": 0.0000131601,
"gnomad_exomes_ac": 27,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6000000238418579,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"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": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.512,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000255266.10",
"gene_symbol": "PDE6A",
"hgnc_id": 8785,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1957C>T",
"hgvs_p": "p.Arg653*"
}
],
"clinvar_disease": "Inborn genetic diseases,Retinal dystrophy,Retinitis pigmentosa,Retinitis pigmentosa 43,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:9",
"phenotype_combined": "Retinitis pigmentosa|Inborn genetic diseases|not provided|Retinal dystrophy|Retinitis pigmentosa 43",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}