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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: 3-132446504-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=132446504&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 132446504,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001329126.2",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC13",
"gene_hgnc_id": 30343,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.His33Arg",
"transcript": "NM_015268.4",
"protein_id": "NP_056083.3",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 2243,
"cds_start": 98,
"cds_end": null,
"cds_length": 6732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000260818.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015268.4"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC13",
"gene_hgnc_id": 30343,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.His33Arg",
"transcript": "ENST00000260818.11",
"protein_id": "ENSP00000260818.6",
"transcript_support_level": 1,
"aa_start": 33,
"aa_end": null,
"aa_length": 2243,
"cds_start": 98,
"cds_end": null,
"cds_length": 6732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015268.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000260818.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC13",
"gene_hgnc_id": 30343,
"hgvs_c": "n.163A>G",
"hgvs_p": null,
"transcript": "ENST00000486798.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000486798.5"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC13",
"gene_hgnc_id": 30343,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.His33Arg",
"transcript": "NM_001329126.2",
"protein_id": "NP_001316055.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 2248,
"cds_start": 98,
"cds_end": null,
"cds_length": 6747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001329126.2"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC13",
"gene_hgnc_id": 30343,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.His33Arg",
"transcript": "XM_047447819.1",
"protein_id": "XP_047303775.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 2248,
"cds_start": 98,
"cds_end": null,
"cds_length": 6747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447819.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC13",
"gene_hgnc_id": 30343,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.His33Arg",
"transcript": "XM_047447820.1",
"protein_id": "XP_047303776.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 2243,
"cds_start": 98,
"cds_end": null,
"cds_length": 6732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447820.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC13",
"gene_hgnc_id": 30343,
"hgvs_c": "n.98A>G",
"hgvs_p": null,
"transcript": "ENST00000650455.1",
"protein_id": "ENSP00000496825.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000650455.1"
}
],
"gene_symbol": "DNAJC13",
"gene_hgnc_id": 30343,
"dbsnp": "rs1933248311",
"frequency_reference_population": 0.0000080787495,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000823568,
"gnomad_genomes_af": 0.00000657523,
"gnomad_exomes_ac": 12,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3697519302368164,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.176,
"revel_prediction": "Benign",
"alphamissense_score": 0.1203,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.13,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.313,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001329126.2",
"gene_symbol": "DNAJC13",
"hgnc_id": 30343,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.98A>G",
"hgvs_p": "p.His33Arg"
}
],
"clinvar_disease": "DNAJC13-related disorder",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "DNAJC13-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}