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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: 1-243270236-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=243270236&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 243270236,
"ref": "G",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_006642.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.199G>T",
"hgvs_p": "p.Glu67*",
"transcript": "NM_006642.5",
"protein_id": "NP_006633.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 713,
"cds_start": 199,
"cds_end": null,
"cds_length": 2142,
"cdna_start": 332,
"cdna_end": null,
"cdna_length": 2581,
"mane_select": "ENST00000366541.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.199G>T",
"hgvs_p": "p.Glu67*",
"transcript": "ENST00000366541.8",
"protein_id": "ENSP00000355499.3",
"transcript_support_level": 1,
"aa_start": 67,
"aa_end": null,
"aa_length": 713,
"cds_start": 199,
"cds_end": null,
"cds_length": 2142,
"cdna_start": 332,
"cdna_end": null,
"cdna_length": 2581,
"mane_select": "NM_006642.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.199G>T",
"hgvs_p": "p.Glu67*",
"transcript": "NM_001350248.2",
"protein_id": "NP_001337177.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 745,
"cds_start": 199,
"cds_end": null,
"cds_length": 2238,
"cdna_start": 332,
"cdna_end": null,
"cdna_length": 2677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "n.352G>T",
"hgvs_p": null,
"transcript": "ENST00000490065.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "n.210G>T",
"hgvs_p": null,
"transcript": "ENST00000491888.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 286,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.-96G>T",
"hgvs_p": null,
"transcript": "NM_001350249.2",
"protein_id": "NP_001337178.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 615,
"cds_start": -4,
"cds_end": null,
"cds_length": 1848,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.-914G>T",
"hgvs_p": null,
"transcript": "NM_001350246.2",
"protein_id": "NP_001337175.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 412,
"cds_start": -4,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.-802G>T",
"hgvs_p": null,
"transcript": "NM_001350247.2",
"protein_id": "NP_001337176.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 412,
"cds_start": -4,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.-1175G>T",
"hgvs_p": null,
"transcript": "NM_001350251.2",
"protein_id": "NP_001337180.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 412,
"cds_start": -4,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"dbsnp": "rs756518004",
"frequency_reference_population": 6.840956e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84096e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3499999940395355,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.471,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_006642.5",
"gene_symbol": "SDCCAG8",
"hgnc_id": 10671,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.199G>T",
"hgvs_p": "p.Glu67*"
}
],
"clinvar_disease": "Bardet-Biedl syndrome 16,Senior-Loken syndrome 7,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Senior-Loken syndrome 7;Bardet-Biedl syndrome 16|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}