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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: 1-230178256-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=230178256&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 230178256,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000366672.5",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.165C>A",
"hgvs_p": "p.Asp55Glu",
"transcript": "NM_004481.5",
"protein_id": "NP_004472.1",
"transcript_support_level": null,
"aa_start": 55,
"aa_end": null,
"aa_length": 571,
"cds_start": 165,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 208,
"cdna_end": null,
"cdna_length": 4423,
"mane_select": "ENST00000366672.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.165C>A",
"hgvs_p": "p.Asp55Glu",
"transcript": "ENST00000366672.5",
"protein_id": "ENSP00000355632.4",
"transcript_support_level": 1,
"aa_start": 55,
"aa_end": null,
"aa_length": 571,
"cds_start": 165,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 208,
"cdna_end": null,
"cdna_length": 4423,
"mane_select": "NM_004481.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.51C>A",
"hgvs_p": "p.Asp17Glu",
"transcript": "NM_001291866.2",
"protein_id": "NP_001278795.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 533,
"cds_start": 51,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 329,
"cdna_end": null,
"cdna_length": 4544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.72C>A",
"hgvs_p": "p.Asp24Glu",
"transcript": "XM_017000964.3",
"protein_id": "XP_016856453.2",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 540,
"cds_start": 72,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 32968,
"cdna_end": null,
"cdna_length": 37183,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "n.128C>A",
"hgvs_p": null,
"transcript": "ENST00000494106.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"dbsnp": "rs1255488508",
"frequency_reference_population": 0.000011771864,
"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.0000116294,
"gnomad_genomes_af": 0.0000131401,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11212471127510071,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.249,
"revel_prediction": "Benign",
"alphamissense_score": 0.0849,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.539,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000366672.5",
"gene_symbol": "GALNT2",
"hgnc_id": 4124,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.165C>A",
"hgvs_p": "p.Asp55Glu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}