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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: 12-52519815-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=52519815&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 52519815,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000252242.9",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "c.482T>G",
"hgvs_p": "p.Ile161Ser",
"transcript": "NM_000424.4",
"protein_id": "NP_000415.2",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 590,
"cds_start": 482,
"cds_end": null,
"cds_length": 1773,
"cdna_start": 580,
"cdna_end": null,
"cdna_length": 2238,
"mane_select": "ENST00000252242.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "c.482T>G",
"hgvs_p": "p.Ile161Ser",
"transcript": "ENST00000252242.9",
"protein_id": "ENSP00000252242.4",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 590,
"cds_start": 482,
"cds_end": null,
"cds_length": 1773,
"cdna_start": 580,
"cdna_end": null,
"cdna_length": 2238,
"mane_select": "NM_000424.4",
"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": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "n.580T>G",
"hgvs_p": null,
"transcript": "ENST00000552629.5",
"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": 2046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "c.152T>G",
"hgvs_p": "p.Ile51Ser",
"transcript": "ENST00000549420.1",
"protein_id": "ENSP00000447209.1",
"transcript_support_level": 5,
"aa_start": 51,
"aa_end": null,
"aa_length": 177,
"cds_start": 152,
"cds_end": null,
"cds_length": 536,
"cdna_start": 227,
"cdna_end": null,
"cdna_length": 611,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "c.377T>G",
"hgvs_p": "p.Ile126Ser",
"transcript": "ENST00000551275.1",
"protein_id": "ENSP00000448041.1",
"transcript_support_level": 4,
"aa_start": 126,
"aa_end": null,
"aa_length": 146,
"cds_start": 377,
"cds_end": null,
"cds_length": 441,
"cdna_start": 475,
"cdna_end": null,
"cdna_length": 539,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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+3150A>C",
"hgvs_p": null,
"transcript": "ENST00000794060.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.381-18353A>C",
"hgvs_p": null,
"transcript": "ENST00000794061.1",
"protein_id": null,
"transcript_support_level": null,
"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": 937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "n.-198T>G",
"hgvs_p": null,
"transcript": "ENST00000551013.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"hgvs_c": "c.*86T>G",
"hgvs_p": null,
"transcript": "ENST00000546577.1",
"protein_id": "ENSP00000449651.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 131,
"cds_start": -4,
"cds_end": null,
"cds_length": 396,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000303401",
"gene_hgnc_id": null,
"hgvs_c": "n.*141A>C",
"hgvs_p": null,
"transcript": "ENST00000794236.1",
"protein_id": null,
"transcript_support_level": null,
"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": 892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KRT5",
"gene_hgnc_id": 6442,
"dbsnp": "rs58058996",
"frequency_reference_population": 0.0000013680939,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136809,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9765487313270569,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.677,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9743,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.33,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.327,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000252242.9",
"gene_symbol": "KRT5",
"hgnc_id": 6442,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.482T>G",
"hgvs_p": "p.Ile161Ser"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000794060.1",
"gene_symbol": "ENSG00000303382",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.550+3150A>C",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000794236.1",
"gene_symbol": "ENSG00000303401",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*141A>C",
"hgvs_p": null
}
],
"clinvar_disease": " localized,Epidermolysis bullosa simplex 1C,Epidermolysis bullosa simplex 2C,KRT5-related disorder,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 O:1",
"phenotype_combined": "not provided|KRT5-related disorder|Epidermolysis bullosa simplex 2C, localized|Epidermolysis bullosa simplex 1C, localized",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}