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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: 6-109443020-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=109443020&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 109443020,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_003080.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.668T>A",
"hgvs_p": "p.Val223Asp",
"transcript": "NM_003080.3",
"protein_id": "NP_003071.2",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 423,
"cds_start": 668,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000258052.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003080.3"
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.668T>A",
"hgvs_p": "p.Val223Asp",
"transcript": "ENST00000258052.8",
"protein_id": "ENSP00000258052.3",
"transcript_support_level": 1,
"aa_start": 223,
"aa_end": null,
"aa_length": 423,
"cds_start": 668,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003080.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000258052.8"
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.650T>A",
"hgvs_p": "p.Val217Asp",
"transcript": "ENST00000882802.1",
"protein_id": "ENSP00000552861.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 417,
"cds_start": 650,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882802.1"
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.578T>A",
"hgvs_p": "p.Val193Asp",
"transcript": "ENST00000882801.1",
"protein_id": "ENSP00000552860.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 393,
"cds_start": 578,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882801.1"
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.356T>A",
"hgvs_p": "p.Val119Asp",
"transcript": "ENST00000458487.1",
"protein_id": "ENSP00000399731.1",
"transcript_support_level": 2,
"aa_start": 119,
"aa_end": null,
"aa_length": 202,
"cds_start": 356,
"cds_end": null,
"cds_length": 611,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000458487.1"
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.353T>A",
"hgvs_p": "p.Val118Asp",
"transcript": "XM_011536079.2",
"protein_id": "XP_011534381.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 318,
"cds_start": 353,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011536079.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "n.1066T>A",
"hgvs_p": null,
"transcript": "XR_942566.3",
"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": "XR_942566.3"
}
],
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"dbsnp": "rs531649765",
"frequency_reference_population": 0.0000013681032,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.0000013681,
"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": 0.7140028476715088,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.276,
"revel_prediction": "Benign",
"alphamissense_score": 0.6069,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.971,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_003080.3",
"gene_symbol": "SMPD2",
"hgnc_id": 11121,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.668T>A",
"hgvs_p": "p.Val223Asp"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}