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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: 20-13093554-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=13093554&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PP2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SPTLC3",
"hgnc_id": 16253,
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Ile",
"inheritance_mode": "AR",
"pathogenic_score": 1,
"score": -1,
"transcript": "NM_018327.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP2,BP4_Moderate",
"acmg_score": -1,
"allele_count_reference_population": 41,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1656,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.23,
"chr": "20",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.2074093222618103,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 552,
"aa_ref": "T",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6191,
"cdna_start": 1099,
"cds_end": null,
"cds_length": 1659,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_018327.4",
"gene_hgnc_id": 16253,
"gene_symbol": "SPTLC3",
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000399002.7",
"protein_coding": true,
"protein_id": "NP_060797.2",
"strand": true,
"transcript": "NM_018327.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 552,
"aa_ref": "T",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6191,
"cdna_start": 1099,
"cds_end": null,
"cds_length": 1659,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000399002.7",
"gene_hgnc_id": 16253,
"gene_symbol": "SPTLC3",
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018327.4",
"protein_coding": true,
"protein_id": "ENSP00000381968.2",
"strand": true,
"transcript": "ENST00000399002.7",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 558,
"aa_ref": "T",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3656,
"cdna_start": 887,
"cds_end": null,
"cds_length": 1677,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000966145.1",
"gene_hgnc_id": 16253,
"gene_symbol": "SPTLC3",
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636204.1",
"strand": true,
"transcript": "ENST00000966145.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 552,
"aa_ref": "T",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6063,
"cdna_start": 971,
"cds_end": null,
"cds_length": 1659,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001349945.2",
"gene_hgnc_id": 16253,
"gene_symbol": "SPTLC3",
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001336874.1",
"strand": true,
"transcript": "NM_001349945.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 523,
"aa_ref": "T",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1956,
"cdna_start": 1099,
"cds_end": null,
"cds_length": 1572,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_011529279.2",
"gene_hgnc_id": 16253,
"gene_symbol": "SPTLC3",
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011527581.1",
"strand": true,
"transcript": "XM_011529279.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 523,
"aa_ref": "T",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1828,
"cdna_start": 971,
"cds_end": null,
"cds_length": 1572,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047440255.1",
"gene_hgnc_id": 16253,
"gene_symbol": "SPTLC3",
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296211.1",
"strand": true,
"transcript": "XM_047440255.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 361,
"aa_ref": "T",
"aa_start": 77,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5400,
"cdna_start": 308,
"cds_end": null,
"cds_length": 1086,
"cds_start": 230,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_011529280.2",
"gene_hgnc_id": 16253,
"gene_symbol": "SPTLC3",
"hgvs_c": "c.230C>T",
"hgvs_p": "p.Thr77Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011527582.1",
"strand": true,
"transcript": "XM_011529280.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 329,
"aa_ref": "T",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1355,
"cdna_start": 1099,
"cds_end": null,
"cds_length": 990,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047440256.1",
"gene_hgnc_id": 16253,
"gene_symbol": "SPTLC3",
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296212.1",
"strand": true,
"transcript": "XM_047440256.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs377121180",
"effect": "missense_variant",
"frequency_reference_population": 0.000025414252,
"gene_hgnc_id": 16253,
"gene_symbol": "SPTLC3",
"gnomad_exomes_ac": 18,
"gnomad_exomes_af": 0.0000123189,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 23,
"gnomad_genomes_af": 0.000151216,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 3.924,
"pos": 13093554,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.486,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_018327.4"
}
]
}