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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: 3-98799538-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=98799538&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 98799538,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_080927.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCBLD2",
"gene_hgnc_id": 24627,
"hgvs_c": "c.2162G>A",
"hgvs_p": "p.Arg721Lys",
"transcript": "NM_080927.4",
"protein_id": "NP_563615.3",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 775,
"cds_start": 2162,
"cds_end": null,
"cds_length": 2328,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000326840.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080927.4"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCBLD2",
"gene_hgnc_id": 24627,
"hgvs_c": "c.2162G>A",
"hgvs_p": "p.Arg721Lys",
"transcript": "ENST00000326840.11",
"protein_id": "ENSP00000321573.6",
"transcript_support_level": 1,
"aa_start": 721,
"aa_end": null,
"aa_length": 775,
"cds_start": 2162,
"cds_end": null,
"cds_length": 2328,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_080927.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000326840.11"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCBLD2",
"gene_hgnc_id": 24627,
"hgvs_c": "c.2204G>A",
"hgvs_p": "p.Arg735Lys",
"transcript": "ENST00000326857.9",
"protein_id": "ENSP00000321646.9",
"transcript_support_level": 1,
"aa_start": 735,
"aa_end": null,
"aa_length": 789,
"cds_start": 2204,
"cds_end": null,
"cds_length": 2370,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000326857.9"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCBLD2",
"gene_hgnc_id": 24627,
"hgvs_c": "c.2024G>A",
"hgvs_p": "p.Arg675Lys",
"transcript": "ENST00000946562.1",
"protein_id": "ENSP00000616621.1",
"transcript_support_level": null,
"aa_start": 675,
"aa_end": null,
"aa_length": 729,
"cds_start": 2024,
"cds_end": null,
"cds_length": 2190,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946562.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCBLD2",
"gene_hgnc_id": 24627,
"hgvs_c": "c.1955G>A",
"hgvs_p": "p.Arg652Lys",
"transcript": "ENST00000926049.1",
"protein_id": "ENSP00000596108.1",
"transcript_support_level": null,
"aa_start": 652,
"aa_end": null,
"aa_length": 706,
"cds_start": 1955,
"cds_end": null,
"cds_length": 2121,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926049.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCBLD2",
"gene_hgnc_id": 24627,
"hgvs_c": "c.1934G>A",
"hgvs_p": "p.Arg645Lys",
"transcript": "ENST00000881287.1",
"protein_id": "ENSP00000551346.1",
"transcript_support_level": null,
"aa_start": 645,
"aa_end": null,
"aa_length": 699,
"cds_start": 1934,
"cds_end": null,
"cds_length": 2100,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881287.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCBLD2",
"gene_hgnc_id": 24627,
"hgvs_c": "c.1796G>A",
"hgvs_p": "p.Arg599Lys",
"transcript": "ENST00000926048.1",
"protein_id": "ENSP00000596107.1",
"transcript_support_level": null,
"aa_start": 599,
"aa_end": null,
"aa_length": 653,
"cds_start": 1796,
"cds_end": null,
"cds_length": 1962,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926048.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCBLD2",
"gene_hgnc_id": 24627,
"hgvs_c": "c.1727G>A",
"hgvs_p": "p.Arg576Lys",
"transcript": "ENST00000926050.1",
"protein_id": "ENSP00000596109.1",
"transcript_support_level": null,
"aa_start": 576,
"aa_end": null,
"aa_length": 630,
"cds_start": 1727,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926050.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCBLD2",
"gene_hgnc_id": 24627,
"hgvs_c": "c.1934G>A",
"hgvs_p": "p.Arg645Lys",
"transcript": "XM_011512419.3",
"protein_id": "XP_011510721.1",
"transcript_support_level": null,
"aa_start": 645,
"aa_end": null,
"aa_length": 699,
"cds_start": 1934,
"cds_end": null,
"cds_length": 2100,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512419.3"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCBLD2",
"gene_hgnc_id": 24627,
"hgvs_c": "c.1844G>A",
"hgvs_p": "p.Arg615Lys",
"transcript": "XM_024453348.2",
"protein_id": "XP_024309116.1",
"transcript_support_level": null,
"aa_start": 615,
"aa_end": null,
"aa_length": 669,
"cds_start": 1844,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453348.2"
},
{
"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": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ST3GAL6",
"gene_hgnc_id": 18080,
"hgvs_c": "c.*32-2011C>T",
"hgvs_p": null,
"transcript": "ENST00000881500.1",
"protein_id": "ENSP00000551559.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 331,
"cds_start": null,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881500.1"
},
{
"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": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ST3GAL6",
"gene_hgnc_id": 18080,
"hgvs_c": "c.*31+5746C>T",
"hgvs_p": null,
"transcript": "ENST00000946763.1",
"protein_id": "ENSP00000616822.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 331,
"cds_start": null,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946763.1"
},
{
"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": "ST3GAL6",
"gene_hgnc_id": 18080,
"hgvs_c": "n.254-1884C>T",
"hgvs_p": null,
"transcript": "ENST00000491912.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000491912.1"
}
],
"gene_symbol": "DCBLD2",
"gene_hgnc_id": 24627,
"dbsnp": "rs772607916",
"frequency_reference_population": 0.000010533895,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.0000109462,
"gnomad_genomes_af": 0.00000657298,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.14136618375778198,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.068,
"revel_prediction": "Benign",
"alphamissense_score": 0.0936,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.914,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": "NM_080927.4",
"gene_symbol": "DCBLD2",
"hgnc_id": 24627,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2162G>A",
"hgvs_p": "p.Arg721Lys"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000881500.1",
"gene_symbol": "ST3GAL6",
"hgnc_id": 18080,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*32-2011C>T",
"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
}