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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: 5-1009547-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=1009547&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 1009547,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_033120.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "NM_033120.4",
"protein_id": "NP_149111.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 451,
"cds_start": 128,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000296849.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_033120.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "ENST00000296849.10",
"protein_id": "ENSP00000296849.5",
"transcript_support_level": 1,
"aa_start": 43,
"aa_end": null,
"aa_length": 451,
"cds_start": 128,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_033120.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000296849.10"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "ENST00000274150.4",
"protein_id": "ENSP00000274150.4",
"transcript_support_level": 1,
"aa_start": 43,
"aa_end": null,
"aa_length": 311,
"cds_start": 128,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000274150.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "ENST00000866687.1",
"protein_id": "ENSP00000536746.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 500,
"cds_start": 128,
"cds_end": null,
"cds_length": 1503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866687.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "ENST00000866688.1",
"protein_id": "ENSP00000536747.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 500,
"cds_start": 128,
"cds_end": null,
"cds_length": 1503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866688.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "ENST00000866690.1",
"protein_id": "ENSP00000536749.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 494,
"cds_start": 128,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866690.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "ENST00000866693.1",
"protein_id": "ENSP00000536752.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 489,
"cds_start": 128,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866693.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.92C>T",
"hgvs_p": "p.Ala31Val",
"transcript": "ENST00000866692.1",
"protein_id": "ENSP00000536751.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 488,
"cds_start": 92,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866692.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "ENST00000866689.1",
"protein_id": "ENSP00000536748.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 469,
"cds_start": 128,
"cds_end": null,
"cds_length": 1410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866689.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "ENST00000866691.1",
"protein_id": "ENSP00000536750.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 452,
"cds_start": 128,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866691.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "ENST00000963996.1",
"protein_id": "ENSP00000634055.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 440,
"cds_start": 128,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963996.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "NM_001271082.2",
"protein_id": "NP_001258011.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 311,
"cds_start": 128,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001271082.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "XM_005248382.4",
"protein_id": "XP_005248439.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 500,
"cds_start": 128,
"cds_end": null,
"cds_length": 1503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005248382.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "XM_011514150.4",
"protein_id": "XP_011512452.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 361,
"cds_start": 128,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514150.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "XM_005248383.5",
"protein_id": "XP_005248440.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 360,
"cds_start": 128,
"cds_end": null,
"cds_length": 1083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005248383.5"
}
],
"gene_symbol": "NKD2",
"gene_hgnc_id": 17046,
"dbsnp": "rs769392378",
"frequency_reference_population": 0.0000037330371,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000373304,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07934042811393738,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.079,
"revel_prediction": "Benign",
"alphamissense_score": 0.0844,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.046,
"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": 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_033120.4",
"gene_symbol": "NKD2",
"hgnc_id": 17046,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val"
}
],
"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
}