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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: 11-11964559-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=11964559&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 11964559,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001018057.2",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.958G>A",
"hgvs_p": "p.Glu320Lys",
"transcript": "NM_001018057.2",
"protein_id": "NP_001018067.1",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 350,
"cds_start": 958,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 2525,
"mane_select": "ENST00000683431.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.958G>A",
"hgvs_p": "p.Glu320Lys",
"transcript": "ENST00000683431.1",
"protein_id": "ENSP00000506835.1",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 350,
"cds_start": 958,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 2525,
"mane_select": "NM_001018057.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.958G>A",
"hgvs_p": "p.Glu320Lys",
"transcript": "ENST00000326932.8",
"protein_id": "ENSP00000314910.4",
"transcript_support_level": 1,
"aa_start": 320,
"aa_end": null,
"aa_length": 350,
"cds_start": 958,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1183,
"cdna_end": null,
"cdna_length": 2636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.958G>A",
"hgvs_p": "p.Glu320Lys",
"transcript": "ENST00000396505.7",
"protein_id": "ENSP00000379762.2",
"transcript_support_level": 1,
"aa_start": 320,
"aa_end": null,
"aa_length": 350,
"cds_start": 958,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1197,
"cdna_end": null,
"cdna_length": 9549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Glu334Lys",
"transcript": "NM_001330220.3",
"protein_id": "NP_001317149.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 364,
"cds_start": 1000,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 1191,
"cdna_end": null,
"cdna_length": 2714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Glu334Lys",
"transcript": "ENST00000525493.5",
"protein_id": "ENSP00000433112.1",
"transcript_support_level": 2,
"aa_start": 334,
"aa_end": null,
"aa_length": 364,
"cds_start": 1000,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 1158,
"cdna_end": null,
"cdna_length": 1326,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.958G>A",
"hgvs_p": "p.Glu320Lys",
"transcript": "NM_013253.5",
"protein_id": "NP_037385.2",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 350,
"cds_start": 958,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1149,
"cdna_end": null,
"cdna_length": 2672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.958G>A",
"hgvs_p": "p.Glu320Lys",
"transcript": "NM_015881.6",
"protein_id": "NP_056965.3",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 350,
"cds_start": 958,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1255,
"cdna_end": null,
"cdna_length": 2778,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Glu334Lys",
"transcript": "XM_017017555.2",
"protein_id": "XP_016873044.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 364,
"cds_start": 1000,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 1128,
"cdna_end": null,
"cdna_length": 2651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Glu334Lys",
"transcript": "XM_047426774.1",
"protein_id": "XP_047282730.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 364,
"cds_start": 1000,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 1134,
"cdna_end": null,
"cdna_length": 2657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.958G>A",
"hgvs_p": "p.Glu320Lys",
"transcript": "XM_006718178.3",
"protein_id": "XP_006718241.1",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 350,
"cds_start": 958,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1086,
"cdna_end": null,
"cdna_length": 2609,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "c.958G>A",
"hgvs_p": "p.Glu320Lys",
"transcript": "XM_047426775.1",
"protein_id": "XP_047282731.1",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 350,
"cds_start": 958,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1092,
"cdna_end": null,
"cdna_length": 2615,
"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": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "n.262-90G>A",
"hgvs_p": null,
"transcript": "ENST00000527132.1",
"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": 1625,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"hgvs_c": "n.*56G>A",
"hgvs_p": null,
"transcript": "ENST00000528188.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DKK3",
"gene_hgnc_id": 2893,
"dbsnp": "rs751011348",
"frequency_reference_population": 6.840591e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84059e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.17170453071594238,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.065,
"revel_prediction": "Benign",
"alphamissense_score": 0.247,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.606,
"phylop100way_prediction": "Uncertain_significance",
"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": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001018057.2",
"gene_symbol": "DKK3",
"hgnc_id": 2893,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.958G>A",
"hgvs_p": "p.Glu320Lys"
}
],
"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
}