← Back to variant description
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: 16-56831918-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=56831918&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 56831918,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000308159.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.1162C>T",
"hgvs_p": "p.Arg388Trp",
"transcript": "NM_014669.5",
"protein_id": "NP_055484.3",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 819,
"cds_start": 1162,
"cds_end": null,
"cds_length": 2460,
"cdna_start": 1259,
"cdna_end": null,
"cdna_length": 8234,
"mane_select": "ENST00000308159.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.1162C>T",
"hgvs_p": "p.Arg388Trp",
"transcript": "ENST00000308159.10",
"protein_id": "ENSP00000310668.5",
"transcript_support_level": 1,
"aa_start": 388,
"aa_end": null,
"aa_length": 819,
"cds_start": 1162,
"cds_end": null,
"cds_length": 2460,
"cdna_start": 1259,
"cdna_end": null,
"cdna_length": 8234,
"mane_select": "NM_014669.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.1162C>T",
"hgvs_p": "p.Arg388Trp",
"transcript": "ENST00000569842.5",
"protein_id": "ENSP00000458101.1",
"transcript_support_level": 5,
"aa_start": 388,
"aa_end": null,
"aa_length": 880,
"cds_start": 1162,
"cds_end": null,
"cds_length": 2643,
"cdna_start": 1258,
"cdna_end": null,
"cdna_length": 2834,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.793C>T",
"hgvs_p": "p.Arg265Trp",
"transcript": "NM_001242795.2",
"protein_id": "NP_001229724.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 696,
"cds_start": 793,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 1251,
"cdna_end": null,
"cdna_length": 8226,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.793C>T",
"hgvs_p": "p.Arg265Trp",
"transcript": "NM_001242796.2",
"protein_id": "NP_001229725.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 696,
"cds_start": 793,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 1282,
"cdna_end": null,
"cdna_length": 2921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.793C>T",
"hgvs_p": "p.Arg265Trp",
"transcript": "ENST00000542526.5",
"protein_id": "ENSP00000440235.1",
"transcript_support_level": 2,
"aa_start": 265,
"aa_end": null,
"aa_length": 696,
"cds_start": 793,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 1282,
"cdna_end": null,
"cdna_length": 8257,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.793C>T",
"hgvs_p": "p.Arg265Trp",
"transcript": "ENST00000564887.5",
"protein_id": "ENSP00000458039.1",
"transcript_support_level": 2,
"aa_start": 265,
"aa_end": null,
"aa_length": 696,
"cds_start": 793,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 1422,
"cdna_end": null,
"cdna_length": 2875,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.541C>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000563858.5",
"protein_id": "ENSP00000455230.1",
"transcript_support_level": 5,
"aa_start": 181,
"aa_end": null,
"aa_length": 228,
"cds_start": 541,
"cds_end": null,
"cds_length": 689,
"cdna_start": 649,
"cdna_end": null,
"cdna_length": 797,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.1162C>T",
"hgvs_p": "p.Arg388Trp",
"transcript": "XM_005256263.4",
"protein_id": "XP_005256320.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 819,
"cds_start": 1162,
"cds_end": null,
"cds_length": 2460,
"cdna_start": 1302,
"cdna_end": null,
"cdna_length": 8277,
"mane_select": null,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "n.404C>T",
"hgvs_p": null,
"transcript": "ENST00000563437.1",
"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": 762,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"dbsnp": "rs145146218",
"frequency_reference_population": 0.0005799012,
"hom_count_reference_population": 3,
"allele_count_reference_population": 936,
"gnomad_exomes_af": 0.000566406,
"gnomad_genomes_af": 0.000709509,
"gnomad_exomes_ac": 828,
"gnomad_genomes_ac": 108,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09350121021270752,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.399,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9084,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.11,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.095,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000308159.10",
"gene_symbol": "NUP93",
"hgnc_id": 28958,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1162C>T",
"hgvs_p": "p.Arg388Trp"
}
],
"clinvar_disease": " type 12,NUP93-related disorder,Nephrotic syndrome,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:5",
"phenotype_combined": "Nephrotic syndrome, type 12|not provided|NUP93-related disorder|Nephrotic syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}