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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: 10-88817847-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=88817847&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 88817847,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001128215.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPM",
"gene_hgnc_id": 23455,
"hgvs_c": "c.953G>A",
"hgvs_p": "p.Arg318Gln",
"transcript": "NM_001128215.1",
"protein_id": "NP_001121687.1",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 423,
"cds_start": 953,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000404743.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001128215.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPM",
"gene_hgnc_id": 23455,
"hgvs_c": "c.953G>A",
"hgvs_p": "p.Arg318Gln",
"transcript": "ENST00000404743.9",
"protein_id": "ENSP00000383901.3",
"transcript_support_level": 1,
"aa_start": 318,
"aa_end": null,
"aa_length": 423,
"cds_start": 953,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001128215.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000404743.9"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPM",
"gene_hgnc_id": 23455,
"hgvs_c": "c.833G>A",
"hgvs_p": "p.Arg278Gln",
"transcript": "ENST00000539337.2",
"protein_id": "ENSP00000440375.1",
"transcript_support_level": 2,
"aa_start": 278,
"aa_end": null,
"aa_length": 383,
"cds_start": 833,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000539337.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPM",
"gene_hgnc_id": 23455,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325Gln",
"transcript": "XM_011539748.4",
"protein_id": "XP_011538050.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 430,
"cds_start": 974,
"cds_end": null,
"cds_length": 1293,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011539748.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPM",
"gene_hgnc_id": 23455,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "XM_011539751.4",
"protein_id": "XP_011538053.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 302,
"cds_start": 590,
"cds_end": null,
"cds_length": 909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011539751.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPM",
"gene_hgnc_id": 23455,
"hgvs_c": "c.404G>A",
"hgvs_p": "p.Arg135Gln",
"transcript": "XM_011539752.4",
"protein_id": "XP_011538054.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 240,
"cds_start": 404,
"cds_end": null,
"cds_length": 723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011539752.4"
}
],
"gene_symbol": "LIPM",
"gene_hgnc_id": 23455,
"dbsnp": "rs569577289",
"frequency_reference_population": 0.000069617774,
"hom_count_reference_population": 0,
"allele_count_reference_population": 108,
"gnomad_exomes_af": 0.0000678991,
"gnomad_genomes_af": 0.0000854173,
"gnomad_exomes_ac": 95,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.023127198219299316,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.058,
"revel_prediction": "Benign",
"alphamissense_score": 0.0754,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.447,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001128215.1",
"gene_symbol": "LIPM",
"hgnc_id": 23455,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.953G>A",
"hgvs_p": "p.Arg318Gln"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}