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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: 15-34342117-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=34342117&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 34342117,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000328848.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NOP10",
"gene_hgnc_id": 14378,
"hgvs_c": "c.55-9C>T",
"hgvs_p": null,
"transcript": "NM_018648.4",
"protein_id": "NP_061118.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 64,
"cds_start": -4,
"cds_end": null,
"cds_length": 195,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 507,
"mane_select": "ENST00000328848.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NOP10",
"gene_hgnc_id": 14378,
"hgvs_c": "c.55-9C>T",
"hgvs_p": null,
"transcript": "ENST00000328848.6",
"protein_id": "ENSP00000332198.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 64,
"cds_start": -4,
"cds_end": null,
"cds_length": 195,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 507,
"mane_select": "NM_018648.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOP10",
"gene_hgnc_id": 14378,
"hgvs_c": "c.70C>T",
"hgvs_p": "p.Leu24Leu",
"transcript": "ENST00000699935.1",
"protein_id": "ENSP00000514698.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 72,
"cds_start": 70,
"cds_end": null,
"cds_length": 219,
"cdna_start": 416,
"cdna_end": null,
"cdna_length": 817,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NOP10",
"gene_hgnc_id": 14378,
"hgvs_c": "c.55-6C>T",
"hgvs_p": null,
"transcript": "ENST00000699926.1",
"protein_id": "ENSP00000514692.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 65,
"cds_start": -4,
"cds_end": null,
"cds_length": 198,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 988,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NOP10",
"gene_hgnc_id": 14378,
"hgvs_c": "c.40-9C>T",
"hgvs_p": null,
"transcript": "ENST00000699937.1",
"protein_id": "ENSP00000514700.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 59,
"cds_start": -4,
"cds_end": null,
"cds_length": 180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 494,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NOP10",
"gene_hgnc_id": 14378,
"hgvs_c": "c.55-9C>T",
"hgvs_p": null,
"transcript": "ENST00000699934.1",
"protein_id": "ENSP00000514697.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 58,
"cds_start": -4,
"cds_end": null,
"cds_length": 177,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NOP10",
"gene_hgnc_id": 14378,
"hgvs_c": "c.55-9C>T",
"hgvs_p": null,
"transcript": "ENST00000699938.1",
"protein_id": "ENSP00000514701.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 55,
"cds_start": -4,
"cds_end": null,
"cds_length": 168,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NOP10",
"gene_hgnc_id": 14378,
"hgvs_c": "c.-12-9C>T",
"hgvs_p": null,
"transcript": "ENST00000699936.1",
"protein_id": "ENSP00000514699.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 42,
"cds_start": -4,
"cds_end": null,
"cds_length": 129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NOP10",
"gene_hgnc_id": 14378,
"hgvs_c": "c.55-67C>T",
"hgvs_p": null,
"transcript": "ENST00000557912.2",
"protein_id": "ENSP00000453475.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 36,
"cds_start": -4,
"cds_end": null,
"cds_length": 111,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 491,
"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": "NOP10",
"gene_hgnc_id": 14378,
"hgvs_c": "n.260-67C>T",
"hgvs_p": null,
"transcript": "ENST00000699939.1",
"protein_id": null,
"transcript_support_level": null,
"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": 591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NOP10",
"gene_hgnc_id": 14378,
"dbsnp": "rs72720799",
"frequency_reference_population": 0.0006933137,
"hom_count_reference_population": 1,
"allele_count_reference_population": 1119,
"gnomad_exomes_af": 0.000729249,
"gnomad_genomes_af": 0.000348203,
"gnomad_exomes_ac": 1066,
"gnomad_genomes_ac": 53,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7400000095367432,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.00800000037997961,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.74,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.296,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000296635349688965,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000328848.6",
"gene_symbol": "NOP10",
"hgnc_id": 14378,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR,Unknown,AD",
"hgvs_c": "c.55-9C>T",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive 1,Dyskeratosis congenita,Hereditary cancer-predisposing syndrome,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:2",
"phenotype_combined": "Dyskeratosis congenita, autosomal recessive 1|not provided|not specified|Hereditary cancer-predisposing syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}