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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: 10-97611587-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=97611587&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 97611587,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_138413.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.912C>A",
"hgvs_p": "p.Ala304Ala",
"transcript": "NM_138413.4",
"protein_id": "NP_612422.2",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 327,
"cds_start": 912,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000370646.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_138413.4"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.912C>A",
"hgvs_p": "p.Ala304Ala",
"transcript": "ENST00000370646.9",
"protein_id": "ENSP00000359680.4",
"transcript_support_level": 1,
"aa_start": 304,
"aa_end": null,
"aa_length": 327,
"cds_start": 912,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_138413.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370646.9"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.423C>A",
"hgvs_p": "p.Ala141Ala",
"transcript": "ENST00000370647.8",
"protein_id": "ENSP00000359681.4",
"transcript_support_level": 1,
"aa_start": 141,
"aa_end": null,
"aa_length": 164,
"cds_start": 423,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370647.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000249967",
"gene_hgnc_id": null,
"hgvs_c": "c.345+9597C>A",
"hgvs_p": null,
"transcript": "ENST00000370649.3",
"protein_id": "ENSP00000359683.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 449,
"cds_start": null,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370649.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.963C>A",
"hgvs_p": "p.Ala321Ala",
"transcript": "ENST00000880786.1",
"protein_id": "ENSP00000550845.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 344,
"cds_start": 963,
"cds_end": null,
"cds_length": 1035,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880786.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.783C>A",
"hgvs_p": "p.Ala261Ala",
"transcript": "ENST00000970078.1",
"protein_id": "ENSP00000640137.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 284,
"cds_start": 783,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970078.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.423C>A",
"hgvs_p": "p.Ala141Ala",
"transcript": "NM_001134670.2",
"protein_id": "NP_001128142.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 164,
"cds_start": 423,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001134670.2"
}
],
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"dbsnp": "rs12261752",
"frequency_reference_population": 0.30425486,
"hom_count_reference_population": 76576,
"allele_count_reference_population": 491057,
"gnomad_exomes_af": 0.304573,
"gnomad_genomes_af": 0.301196,
"gnomad_exomes_ac": 445215,
"gnomad_genomes_ac": 45842,
"gnomad_exomes_homalt": 69495,
"gnomad_genomes_homalt": 7081,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.23999999463558197,
"computational_prediction_selected": "Benign",
"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": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.248,
"phylop100way_prediction": "Benign",
"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": -18,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_138413.4",
"gene_symbol": "HOGA1",
"hgnc_id": 25155,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.912C>A",
"hgvs_p": "p.Ala304Ala"
},
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000370649.3",
"gene_symbol": "ENSG00000249967",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.345+9597C>A",
"hgvs_p": null
}
],
"clinvar_disease": "Primary hyperoxaluria type 3,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:7",
"phenotype_combined": "Primary hyperoxaluria type 3|not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}