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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: 16-56758527-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=56758527&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 56758527,
"ref": "T",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000308159.10",
"consequences": [
{
"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": 22,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.180-11T>A",
"hgvs_p": null,
"transcript": "NM_014669.5",
"protein_id": "NP_055484.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 819,
"cds_start": -4,
"cds_end": null,
"cds_length": 2460,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8234,
"mane_select": "ENST00000308159.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.180-11T>A",
"hgvs_p": null,
"transcript": "ENST00000308159.10",
"protein_id": "ENSP00000310668.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 819,
"cds_start": -4,
"cds_end": null,
"cds_length": 2460,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8234,
"mane_select": "NM_014669.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 23,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.180-11T>A",
"hgvs_p": null,
"transcript": "ENST00000569842.5",
"protein_id": "ENSP00000458101.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 880,
"cds_start": -4,
"cds_end": null,
"cds_length": 2643,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2834,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.19+10261T>A",
"hgvs_p": null,
"transcript": "ENST00000563858.5",
"protein_id": "ENSP00000455230.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 228,
"cds_start": -4,
"cds_end": null,
"cds_length": 689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 797,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.180-11T>A",
"hgvs_p": null,
"transcript": "ENST00000568656.5",
"protein_id": "ENSP00000454285.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 177,
"cds_start": -4,
"cds_end": null,
"cds_length": 535,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.180-11T>A",
"hgvs_p": null,
"transcript": "ENST00000566315.5",
"protein_id": "ENSP00000456264.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 150,
"cds_start": -4,
"cds_end": null,
"cds_length": 454,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.180-11T>A",
"hgvs_p": null,
"transcript": "ENST00000562496.5",
"protein_id": "ENSP00000457902.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 135,
"cds_start": -4,
"cds_end": null,
"cds_length": 409,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.78-11T>A",
"hgvs_p": null,
"transcript": "ENST00000566678.1",
"protein_id": "ENSP00000454935.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 131,
"cds_start": -4,
"cds_end": null,
"cds_length": 396,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 442,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.-190-11T>A",
"hgvs_p": null,
"transcript": "ENST00000569863.5",
"protein_id": "ENSP00000454587.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 124,
"cds_start": -4,
"cds_end": null,
"cds_length": 377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 22,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"hgvs_c": "c.180-11T>A",
"hgvs_p": null,
"transcript": "XM_005256263.4",
"protein_id": "XP_005256320.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 819,
"cds_start": -4,
"cds_end": null,
"cds_length": 2460,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NUP93",
"gene_hgnc_id": 28958,
"dbsnp": "rs138944474",
"frequency_reference_population": 0.0010716188,
"hom_count_reference_population": 28,
"allele_count_reference_population": 1711,
"gnomad_exomes_af": 0.00100804,
"gnomad_genomes_af": 0.0016747,
"gnomad_exomes_ac": 1456,
"gnomad_genomes_ac": 255,
"gnomad_exomes_homalt": 21,
"gnomad_genomes_homalt": 7,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.800000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.527999997138977,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.8,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.132,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.914799605131768,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000308159.10",
"gene_symbol": "NUP93",
"hgnc_id": 28958,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.180-11T>A",
"hgvs_p": null
}
],
"clinvar_disease": " type 12,Nephrotic syndrome,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Nephrotic syndrome, type 12|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}