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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: 2-169509953-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=169509953&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 169509953,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006063.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLHL41",
"gene_hgnc_id": 16905,
"hgvs_c": "c.175C>T",
"hgvs_p": "p.Arg59Cys",
"transcript": "NM_006063.3",
"protein_id": "NP_006054.2",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 606,
"cds_start": 175,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000284669.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006063.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLHL41",
"gene_hgnc_id": 16905,
"hgvs_c": "c.175C>T",
"hgvs_p": "p.Arg59Cys",
"transcript": "ENST00000284669.2",
"protein_id": "ENSP00000284669.1",
"transcript_support_level": 1,
"aa_start": 59,
"aa_end": null,
"aa_length": 606,
"cds_start": 175,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006063.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000284669.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251569",
"gene_hgnc_id": null,
"hgvs_c": "c.925-4621C>T",
"hgvs_p": null,
"transcript": "ENST00000513963.1",
"protein_id": "ENSP00000424363.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 544,
"cds_start": null,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000513963.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLHL41",
"gene_hgnc_id": 16905,
"hgvs_c": "c.175C>T",
"hgvs_p": "p.Arg59Cys",
"transcript": "ENST00000946624.1",
"protein_id": "ENSP00000616683.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 617,
"cds_start": 175,
"cds_end": null,
"cds_length": 1854,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946624.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLHL41",
"gene_hgnc_id": 16905,
"hgvs_c": "c.175C>T",
"hgvs_p": "p.Arg59Cys",
"transcript": "ENST00000946625.1",
"protein_id": "ENSP00000616684.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 557,
"cds_start": 175,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946625.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLHL41",
"gene_hgnc_id": 16905,
"hgvs_c": "c.175C>T",
"hgvs_p": "p.Arg59Cys",
"transcript": "ENST00000946627.1",
"protein_id": "ENSP00000616686.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 544,
"cds_start": 175,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946627.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLHL41",
"gene_hgnc_id": 16905,
"hgvs_c": "c.175C>T",
"hgvs_p": "p.Arg59Cys",
"transcript": "ENST00000946626.1",
"protein_id": "ENSP00000616685.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 495,
"cds_start": 175,
"cds_end": null,
"cds_length": 1488,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946626.1"
}
],
"gene_symbol": "KLHL41",
"gene_hgnc_id": 16905,
"dbsnp": "rs547547946",
"frequency_reference_population": 0.00004584729,
"hom_count_reference_population": 0,
"allele_count_reference_population": 74,
"gnomad_exomes_af": 0.0000444641,
"gnomad_genomes_af": 0.0000591327,
"gnomad_exomes_ac": 65,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9048808813095093,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.669,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8609,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.515,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate,BS1_Supporting",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006063.3",
"gene_symbol": "KLHL41",
"hgnc_id": 16905,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.175C>T",
"hgvs_p": "p.Arg59Cys"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000513963.1",
"gene_symbol": "ENSG00000251569",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.925-4621C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Nemaline myopathy 9,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Nemaline myopathy 9|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}