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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: 12-52516824-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=52516824&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 52516824,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000424.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Glu418Lys",
"transcript": "NM_000424.4",
"protein_id": "NP_000415.2",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 590,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000252242.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000424.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Glu418Lys",
"transcript": "ENST00000252242.9",
"protein_id": "ENSP00000252242.4",
"transcript_support_level": 1,
"aa_start": 418,
"aa_end": null,
"aa_length": 590,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000424.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000252242.9"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "n.1350G>A",
"hgvs_p": null,
"transcript": "ENST00000552629.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000552629.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "c.373G>A",
"hgvs_p": "p.Glu125Lys",
"transcript": "ENST00000548409.5",
"protein_id": "ENSP00000448767.1",
"transcript_support_level": 3,
"aa_start": 125,
"aa_end": null,
"aa_length": 200,
"cds_start": 373,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000548409.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "n.630G>A",
"hgvs_p": null,
"transcript": "ENST00000547890.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000547890.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "n.459G>A",
"hgvs_p": null,
"transcript": "ENST00000549511.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000549511.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000303382",
"gene_hgnc_id": null,
"hgvs_c": "n.550+159C>T",
"hgvs_p": null,
"transcript": "ENST00000794060.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000794060.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000303382",
"gene_hgnc_id": null,
"hgvs_c": "n.380+19396C>T",
"hgvs_p": null,
"transcript": "ENST00000794061.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000794061.1"
}
],
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"dbsnp": "rs121912476",
"frequency_reference_population": 0.000019206369,
"hom_count_reference_population": 0,
"allele_count_reference_population": 31,
"gnomad_exomes_af": 0.0000198375,
"gnomad_genomes_af": 0.0000131434,
"gnomad_exomes_ac": 29,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9870103597640991,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.907,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9522,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.41,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.048,
"phylop100way_prediction": "Uncertain_significance",
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PP3_Strong,BS1_Supporting",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 1,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PP3_Strong",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000424.4",
"gene_symbol": "KRT5",
"hgnc_id": 6442,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Glu418Lys"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000794060.1",
"gene_symbol": "ENSG00000303382",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.550+159C>T",
"hgvs_p": null
}
],
"clinvar_disease": " localized, modifier of,Epidermolysis bullosa simplex 2C,not provided",
"clinvar_classification": "risk factor",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "not provided|Epidermolysis bullosa simplex 2C, localized, modifier of",
"pathogenicity_classification_combined": "risk factor",
"custom_annotations": null
}
],
"message": null
}