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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: 11-112228591-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=112228591&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 112228591,
"ref": "C",
"alt": "G",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000280362.8",
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTS",
"gene_hgnc_id": 9689,
"hgvs_c": "c.84-3C>G",
"hgvs_p": null,
"transcript": "NM_000317.3",
"protein_id": "NP_000308.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 145,
"cds_start": -4,
"cds_end": null,
"cds_length": 438,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 872,
"mane_select": "ENST00000280362.8",
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTS",
"gene_hgnc_id": 9689,
"hgvs_c": "c.84-3C>G",
"hgvs_p": null,
"transcript": "ENST00000280362.8",
"protein_id": "ENSP00000280362.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 145,
"cds_start": -4,
"cds_end": null,
"cds_length": 438,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 872,
"mane_select": "NM_000317.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTS",
"gene_hgnc_id": 9689,
"hgvs_c": "n.159-3C>G",
"hgvs_p": null,
"transcript": "ENST00000525645.1",
"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": 1069,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTS",
"gene_hgnc_id": 9689,
"hgvs_c": "n.84-3C>G",
"hgvs_p": null,
"transcript": "ENST00000531673.5",
"protein_id": "ENSP00000433469.1",
"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": 986,
"mane_select": null,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "PTS",
"gene_hgnc_id": 9689,
"hgvs_c": "c.-121-3C>G",
"hgvs_p": null,
"transcript": "ENST00000524931.1",
"protein_id": "ENSP00000434688.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 77,
"cds_start": -4,
"cds_end": null,
"cds_length": 234,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 696,
"mane_select": null,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTS",
"gene_hgnc_id": 9689,
"hgvs_c": "c.84-3C>G",
"hgvs_p": null,
"transcript": "ENST00000525803.1",
"protein_id": "ENSP00000431750.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 61,
"cds_start": -4,
"cds_end": null,
"cds_length": 186,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 625,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTS",
"gene_hgnc_id": 9689,
"hgvs_c": "n.84-3C>G",
"hgvs_p": null,
"transcript": "ENST00000528679.5",
"protein_id": "ENSP00000435895.1",
"transcript_support_level": 2,
"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": 846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTS",
"gene_hgnc_id": 9689,
"dbsnp": "rs1230781262",
"frequency_reference_population": 0.000010543644,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.00000938499,
"gnomad_genomes_af": 0.0000226737,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.550000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.8759999871253967,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.462,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.54,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.995926697312049,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000280362.8",
"gene_symbol": "PTS",
"hgnc_id": 9689,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.84-3C>G",
"hgvs_p": null
}
],
"clinvar_disease": "6-Pyruvoyl-tetrahydrobiopterin synthase deficiency,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8",
"phenotype_combined": "6-Pyruvoyl-tetrahydrobiopterin synthase deficiency|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}