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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: 5-136046358-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=136046358&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 136046358,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000358.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGFBI",
"gene_hgnc_id": 11771,
"hgvs_c": "c.322G>A",
"hgvs_p": "p.Glu108Lys",
"transcript": "NM_000358.3",
"protein_id": "NP_000349.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 683,
"cds_start": 322,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000442011.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000358.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGFBI",
"gene_hgnc_id": 11771,
"hgvs_c": "c.322G>A",
"hgvs_p": "p.Glu108Lys",
"transcript": "ENST00000442011.7",
"protein_id": "ENSP00000416330.2",
"transcript_support_level": 1,
"aa_start": 108,
"aa_end": null,
"aa_length": 683,
"cds_start": 322,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000358.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000442011.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGFBI",
"gene_hgnc_id": 11771,
"hgvs_c": "n.479G>A",
"hgvs_p": null,
"transcript": "ENST00000504185.5",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000504185.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGFBI",
"gene_hgnc_id": 11771,
"hgvs_c": "n.387G>A",
"hgvs_p": null,
"transcript": "ENST00000506699.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000506699.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGFBI",
"gene_hgnc_id": 11771,
"hgvs_c": "n.238G>A",
"hgvs_p": null,
"transcript": "ENST00000507018.5",
"protein_id": "ENSP00000421540.1",
"transcript_support_level": 5,
"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": "ENST00000507018.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGFBI",
"gene_hgnc_id": 11771,
"hgvs_c": "n.614G>A",
"hgvs_p": null,
"transcript": "ENST00000515433.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000515433.1"
}
],
"gene_symbol": "TGFBI",
"gene_hgnc_id": 11771,
"dbsnp": "rs188322933",
"frequency_reference_population": 0.000071877,
"hom_count_reference_population": 1,
"allele_count_reference_population": 116,
"gnomad_exomes_af": 0.0000752568,
"gnomad_genomes_af": 0.0000394203,
"gnomad_exomes_ac": 110,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.23150992393493652,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.369,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1412,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.607,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": "Likely_benign",
"acmg_criteria": "PM1,BP4_Moderate,BS2_Supporting",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Moderate",
"BS2_Supporting"
],
"verdict": "Likely_benign",
"transcript": "NM_000358.3",
"gene_symbol": "TGFBI",
"hgnc_id": 11771,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.322G>A",
"hgvs_p": "p.Glu108Lys"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}