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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: 9-74782398-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=74782398&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 74782398,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000360774.6",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM6",
"gene_hgnc_id": 17995,
"hgvs_c": "c.3173A>G",
"hgvs_p": "p.Tyr1058Cys",
"transcript": "NM_017662.5",
"protein_id": "NP_060132.3",
"transcript_support_level": null,
"aa_start": 1058,
"aa_end": null,
"aa_length": 2022,
"cds_start": 3173,
"cds_end": null,
"cds_length": 6069,
"cdna_start": 3238,
"cdna_end": null,
"cdna_length": 8252,
"mane_select": "ENST00000360774.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM6",
"gene_hgnc_id": 17995,
"hgvs_c": "c.3173A>G",
"hgvs_p": "p.Tyr1058Cys",
"transcript": "ENST00000360774.6",
"protein_id": "ENSP00000354006.1",
"transcript_support_level": 1,
"aa_start": 1058,
"aa_end": null,
"aa_length": 2022,
"cds_start": 3173,
"cds_end": null,
"cds_length": 6069,
"cdna_start": 3238,
"cdna_end": null,
"cdna_length": 8252,
"mane_select": "NM_017662.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM6",
"gene_hgnc_id": 17995,
"hgvs_c": "c.3158A>G",
"hgvs_p": "p.Tyr1053Cys",
"transcript": "ENST00000361255.7",
"protein_id": "ENSP00000354962.3",
"transcript_support_level": 1,
"aa_start": 1053,
"aa_end": null,
"aa_length": 2017,
"cds_start": 3158,
"cds_end": null,
"cds_length": 6054,
"cdna_start": 3257,
"cdna_end": null,
"cdna_length": 8271,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM6",
"gene_hgnc_id": 17995,
"hgvs_c": "c.3158A>G",
"hgvs_p": "p.Tyr1053Cys",
"transcript": "ENST00000449912.6",
"protein_id": "ENSP00000396672.2",
"transcript_support_level": 1,
"aa_start": 1053,
"aa_end": null,
"aa_length": 2017,
"cds_start": 3158,
"cds_end": null,
"cds_length": 6054,
"cdna_start": 3230,
"cdna_end": null,
"cdna_length": 8244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM6",
"gene_hgnc_id": 17995,
"hgvs_c": "c.3158A>G",
"hgvs_p": "p.Tyr1053Cys",
"transcript": "NM_001177310.2",
"protein_id": "NP_001170781.1",
"transcript_support_level": null,
"aa_start": 1053,
"aa_end": null,
"aa_length": 2017,
"cds_start": 3158,
"cds_end": null,
"cds_length": 6054,
"cdna_start": 3230,
"cdna_end": null,
"cdna_length": 8244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM6",
"gene_hgnc_id": 17995,
"hgvs_c": "c.3158A>G",
"hgvs_p": "p.Tyr1053Cys",
"transcript": "NM_001177311.2",
"protein_id": "NP_001170782.1",
"transcript_support_level": null,
"aa_start": 1053,
"aa_end": null,
"aa_length": 2017,
"cds_start": 3158,
"cds_end": null,
"cds_length": 6054,
"cdna_start": 3257,
"cdna_end": null,
"cdna_length": 8271,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM6",
"gene_hgnc_id": 17995,
"hgvs_c": "n.3173A>G",
"hgvs_p": null,
"transcript": "ENST00000715553.1",
"protein_id": "ENSP00000520473.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TRPM6",
"gene_hgnc_id": 17995,
"dbsnp": "rs797045204",
"frequency_reference_population": 0.000003420431,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342043,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5221454501152039,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.376,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9049,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.13,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.234,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": "ENST00000360774.6",
"gene_symbol": "TRPM6",
"hgnc_id": 17995,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3173A>G",
"hgvs_p": "p.Tyr1058Cys"
}
],
"clinvar_disease": "Inborn genetic diseases,Intestinal hypomagnesemia 1",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Intestinal hypomagnesemia 1|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}