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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: 17-28734066-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=28734066&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 28734066,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_178170.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK8",
"gene_hgnc_id": 13387,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Glu44Val",
"transcript": "NM_178170.3",
"protein_id": "NP_835464.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 692,
"cds_start": 131,
"cds_end": null,
"cds_length": 2079,
"cdna_start": 157,
"cdna_end": null,
"cdna_length": 3573,
"mane_select": "ENST00000268766.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK8",
"gene_hgnc_id": 13387,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Glu44Val",
"transcript": "ENST00000268766.11",
"protein_id": "ENSP00000268766.6",
"transcript_support_level": 1,
"aa_start": 44,
"aa_end": null,
"aa_length": 692,
"cds_start": 131,
"cds_end": null,
"cds_length": 2079,
"cdna_start": 157,
"cdna_end": null,
"cdna_length": 3573,
"mane_select": "NM_178170.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK8",
"gene_hgnc_id": 13387,
"hgvs_c": "c.14A>T",
"hgvs_p": "p.Glu5Val",
"transcript": "ENST00000579060.5",
"protein_id": "ENSP00000466896.1",
"transcript_support_level": 3,
"aa_start": 5,
"aa_end": null,
"aa_length": 166,
"cds_start": 14,
"cds_end": null,
"cds_length": 501,
"cdna_start": 160,
"cdna_end": null,
"cdna_length": 647,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK8",
"gene_hgnc_id": 13387,
"hgvs_c": "c.14A>T",
"hgvs_p": "p.Glu5Val",
"transcript": "ENST00000579671.5",
"protein_id": "ENSP00000467335.1",
"transcript_support_level": 3,
"aa_start": 5,
"aa_end": null,
"aa_length": 164,
"cds_start": 14,
"cds_end": null,
"cds_length": 497,
"cdna_start": 160,
"cdna_end": null,
"cdna_length": 643,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK8",
"gene_hgnc_id": 13387,
"hgvs_c": "n.131A>T",
"hgvs_p": null,
"transcript": "ENST00000543014.1",
"protein_id": "ENSP00000465859.1",
"transcript_support_level": 2,
"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": 2055,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK8",
"gene_hgnc_id": 13387,
"hgvs_c": "n.131A>T",
"hgvs_p": null,
"transcript": "ENST00000581000.1",
"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": 590,
"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": "NEK8",
"gene_hgnc_id": 13387,
"hgvs_c": "n.168A>T",
"hgvs_p": null,
"transcript": "ENST00000584342.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 828,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK8",
"gene_hgnc_id": 13387,
"hgvs_c": "n.129A>T",
"hgvs_p": null,
"transcript": "ENST00000593261.1",
"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": 547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000265073",
"gene_hgnc_id": null,
"hgvs_c": "n.418-1079T>A",
"hgvs_p": null,
"transcript": "ENST00000584779.1",
"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": 442,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NEK8",
"gene_hgnc_id": 13387,
"dbsnp": "rs202217310",
"frequency_reference_population": 0.000012390622,
"hom_count_reference_population": 0,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.0000129969,
"gnomad_genomes_af": 0.00000656866,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7250776886940002,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.625,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.963,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9,
"phylop100way_prediction": "Pathogenic",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_178170.3",
"gene_symbol": "NEK8",
"hgnc_id": 13387,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Glu44Val"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000584779.1",
"gene_symbol": "ENSG00000265073",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.418-1079T>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Nephronophthisis 9,Polycystic kidney disease 8,Renal-hepatic-pancreatic dysplasia 2",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Inborn genetic diseases|Renal-hepatic-pancreatic dysplasia 2;Nephronophthisis 9;Polycystic kidney disease 8",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}