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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: 4-118138210-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=118138210&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 118138210,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004784.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.1381C>T",
"hgvs_p": "p.Arg461Trp",
"transcript": "NM_004784.3",
"protein_id": "NP_004775.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 873,
"cds_start": 1381,
"cds_end": null,
"cds_length": 2622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000296499.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004784.3"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.1381C>T",
"hgvs_p": "p.Arg461Trp",
"transcript": "ENST00000296499.6",
"protein_id": "ENSP00000296499.5",
"transcript_support_level": 1,
"aa_start": 461,
"aa_end": null,
"aa_length": 873,
"cds_start": 1381,
"cds_end": null,
"cds_length": 2622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004784.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000296499.6"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.1381C>T",
"hgvs_p": "p.Arg461Trp",
"transcript": "ENST00000852871.1",
"protein_id": "ENSP00000522930.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 873,
"cds_start": 1381,
"cds_end": null,
"cds_length": 2622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852871.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.1381C>T",
"hgvs_p": "p.Arg461Trp",
"transcript": "XM_017008839.3",
"protein_id": "XP_016864328.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 899,
"cds_start": 1381,
"cds_end": null,
"cds_length": 2700,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008839.3"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.1381C>T",
"hgvs_p": "p.Arg461Trp",
"transcript": "XM_017008840.3",
"protein_id": "XP_016864329.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 899,
"cds_start": 1381,
"cds_end": null,
"cds_length": 2700,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008840.3"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.1381C>T",
"hgvs_p": "p.Arg461Trp",
"transcript": "XM_006714416.4",
"protein_id": "XP_006714479.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 873,
"cds_start": 1381,
"cds_end": null,
"cds_length": 2622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006714416.4"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.1381C>T",
"hgvs_p": "p.Arg461Trp",
"transcript": "XM_011532415.4",
"protein_id": "XP_011530717.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 524,
"cds_start": 1381,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532415.4"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.241C>T",
"hgvs_p": "p.Arg81Trp",
"transcript": "XM_017008841.2",
"protein_id": "XP_016864330.1",
"transcript_support_level": null,
"aa_start": 81,
"aa_end": null,
"aa_length": 519,
"cds_start": 241,
"cds_end": null,
"cds_length": 1560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008841.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.241C>T",
"hgvs_p": "p.Arg81Trp",
"transcript": "XM_017008844.2",
"protein_id": "XP_016864333.1",
"transcript_support_level": null,
"aa_start": 81,
"aa_end": null,
"aa_length": 519,
"cds_start": 241,
"cds_end": null,
"cds_length": 1560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008844.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.241C>T",
"hgvs_p": "p.Arg81Trp",
"transcript": "XM_047416414.1",
"protein_id": "XP_047272370.1",
"transcript_support_level": null,
"aa_start": 81,
"aa_end": null,
"aa_length": 519,
"cds_start": 241,
"cds_end": null,
"cds_length": 1560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416414.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.1381C>T",
"hgvs_p": "p.Arg461Trp",
"transcript": "XM_011532416.4",
"protein_id": "XP_011530718.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 516,
"cds_start": 1381,
"cds_end": null,
"cds_length": 1551,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532416.4"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.1381C>T",
"hgvs_p": "p.Arg461Trp",
"transcript": "XM_047416415.1",
"protein_id": "XP_047272371.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 516,
"cds_start": 1381,
"cds_end": null,
"cds_length": 1551,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416415.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "XM_017008843.2",
"protein_id": "XP_016864332.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 484,
"cds_start": 136,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008843.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "n.2126C>T",
"hgvs_p": null,
"transcript": "NR_146513.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_146513.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"hgvs_c": "n.1643C>T",
"hgvs_p": null,
"transcript": "NR_146514.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_146514.2"
},
{
"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": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000297398",
"gene_hgnc_id": 58877,
"hgvs_c": "n.406-1475G>A",
"hgvs_p": null,
"transcript": "ENST00000747715.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000747715.1"
},
{
"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": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000297398",
"gene_hgnc_id": 58877,
"hgvs_c": "n.402-4601G>A",
"hgvs_p": null,
"transcript": "ENST00000747716.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000747716.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC107986307",
"gene_hgnc_id": null,
"hgvs_c": "n.268-1475G>A",
"hgvs_p": null,
"transcript": "XR_007058241.1",
"protein_id": null,
"transcript_support_level": null,
"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": "XR_007058241.1"
}
],
"gene_symbol": "NDST3",
"gene_hgnc_id": 7682,
"dbsnp": "rs149894200",
"frequency_reference_population": 0.00003222624,
"hom_count_reference_population": 0,
"allele_count_reference_population": 52,
"gnomad_exomes_af": 0.0000335266,
"gnomad_genomes_af": 0.0000197283,
"gnomad_exomes_ac": 49,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9082826972007751,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.25,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.466,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9835,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.251,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.25,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004784.3",
"gene_symbol": "NDST3",
"hgnc_id": 7682,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1381C>T",
"hgvs_p": "p.Arg461Trp"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000747715.1",
"gene_symbol": "ENSG00000297398",
"hgnc_id": 58877,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.406-1475G>A",
"hgvs_p": null
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007058241.1",
"gene_symbol": "LOC107986307",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.268-1475G>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
}