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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: 14-21033889-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=21033889&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 21033889,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000382951.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASE13",
"gene_hgnc_id": 25285,
"hgvs_c": "c.400C>T",
"hgvs_p": "p.Leu134Phe",
"transcript": "NM_001012264.4",
"protein_id": "NP_001012264.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 156,
"cds_start": 400,
"cds_end": null,
"cds_length": 471,
"cdna_start": 560,
"cdna_end": null,
"cdna_length": 1631,
"mane_select": "ENST00000382951.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASE13",
"gene_hgnc_id": 25285,
"hgvs_c": "c.400C>T",
"hgvs_p": "p.Leu134Phe",
"transcript": "ENST00000382951.4",
"protein_id": "ENSP00000372410.3",
"transcript_support_level": 1,
"aa_start": 134,
"aa_end": null,
"aa_length": 156,
"cds_start": 400,
"cds_end": null,
"cds_length": 471,
"cdna_start": 560,
"cdna_end": null,
"cdna_length": 1631,
"mane_select": "NM_001012264.4",
"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": "ENSG00000255472",
"gene_hgnc_id": null,
"hgvs_c": "n.486G>A",
"hgvs_p": null,
"transcript": "ENST00000531638.1",
"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": 492,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NDRG2",
"gene_hgnc_id": 14460,
"hgvs_c": "c.25-10568C>T",
"hgvs_p": null,
"transcript": "NM_001282211.2",
"protein_id": "NP_001269140.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 367,
"cds_start": -4,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NDRG2",
"gene_hgnc_id": 14460,
"hgvs_c": "c.25-10568C>T",
"hgvs_p": null,
"transcript": "ENST00000403829.7",
"protein_id": "ENSP00000385889.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 367,
"cds_start": -4,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NDRG2",
"gene_hgnc_id": 14460,
"hgvs_c": "c.-6-10568C>T",
"hgvs_p": null,
"transcript": "ENST00000555026.5",
"protein_id": "ENSP00000451274.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 272,
"cds_start": -4,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1162,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TPPP2",
"gene_hgnc_id": 19293,
"hgvs_c": "c.328-2302G>A",
"hgvs_p": null,
"transcript": "ENST00000472458.5",
"protein_id": "ENSP00000423171.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 136,
"cds_start": -4,
"cds_end": null,
"cds_length": 411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TPPP2",
"gene_hgnc_id": 19293,
"hgvs_c": "c.*13+1509G>A",
"hgvs_p": null,
"transcript": "ENST00000481535.5",
"protein_id": "ENSP00000421438.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 119,
"cds_start": -4,
"cds_end": null,
"cds_length": 360,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TPPP2",
"gene_hgnc_id": 19293,
"hgvs_c": "c.*13+1509G>A",
"hgvs_p": null,
"transcript": "ENST00000555751.1",
"protein_id": "ENSP00000451899.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 62,
"cds_start": -4,
"cds_end": null,
"cds_length": 189,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TPPP2",
"gene_hgnc_id": 19293,
"hgvs_c": "n.301-1905G>A",
"hgvs_p": null,
"transcript": "ENST00000495665.2",
"protein_id": "ENSP00000436874.1",
"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": 687,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TPPP2",
"gene_hgnc_id": 19293,
"hgvs_c": "n.564-2302G>A",
"hgvs_p": null,
"transcript": "ENST00000529496.1",
"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": 647,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TPPP2",
"gene_hgnc_id": 19293,
"hgvs_c": "c.328-2302G>A",
"hgvs_p": null,
"transcript": "XM_011536416.2",
"protein_id": "XP_011534718.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 157,
"cds_start": -4,
"cds_end": null,
"cds_length": 474,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 646,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "TPPP2",
"gene_hgnc_id": 19293,
"hgvs_c": "c.*13+1509G>A",
"hgvs_p": null,
"transcript": "XM_011536420.3",
"protein_id": "XP_011534722.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 124,
"cds_start": -4,
"cds_end": null,
"cds_length": 375,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RNASE13",
"gene_hgnc_id": 25285,
"dbsnp": "rs201533703",
"frequency_reference_population": 0.000105325766,
"hom_count_reference_population": 1,
"allele_count_reference_population": 170,
"gnomad_exomes_af": 0.000107398,
"gnomad_genomes_af": 0.0000854229,
"gnomad_exomes_ac": 157,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01733410358428955,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.261,
"revel_prediction": "Benign",
"alphamissense_score": 0.4169,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.134,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000382951.4",
"gene_symbol": "RNASE13",
"hgnc_id": 25285,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.400C>T",
"hgvs_p": "p.Leu134Phe"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000531638.1",
"gene_symbol": "ENSG00000255472",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.486G>A",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001282211.2",
"gene_symbol": "NDRG2",
"hgnc_id": 14460,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.25-10568C>T",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000472458.5",
"gene_symbol": "TPPP2",
"hgnc_id": 19293,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.328-2302G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}