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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: 16-89812-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=89812&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 89812,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000611875.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Glu418Lys",
"transcript": "NM_001077350.3",
"protein_id": "NP_001070818.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 569,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1710,
"cdna_start": 1351,
"cdna_end": null,
"cdna_length": 3128,
"mane_select": "ENST00000611875.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Glu418Lys",
"transcript": "ENST00000611875.5",
"protein_id": "ENSP00000478273.1",
"transcript_support_level": 5,
"aa_start": 418,
"aa_end": null,
"aa_length": 569,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1710,
"cdna_start": 1351,
"cdna_end": null,
"cdna_length": 3128,
"mane_select": "NM_001077350.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.1177G>A",
"hgvs_p": "p.Glu393Lys",
"transcript": "ENST00000399953.7",
"protein_id": "ENSP00000382834.4",
"transcript_support_level": 1,
"aa_start": 393,
"aa_end": null,
"aa_length": 544,
"cds_start": 1177,
"cds_end": null,
"cds_length": 1635,
"cdna_start": 1422,
"cdna_end": null,
"cdna_length": 2784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "n.*837G>A",
"hgvs_p": null,
"transcript": "ENST00000621703.4",
"protein_id": "ENSP00000477801.1",
"transcript_support_level": 1,
"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": 2812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "n.*837G>A",
"hgvs_p": null,
"transcript": "ENST00000621703.4",
"protein_id": "ENSP00000477801.1",
"transcript_support_level": 1,
"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": 2812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.1177G>A",
"hgvs_p": "p.Glu393Lys",
"transcript": "NM_001243248.2",
"protein_id": "NP_001230177.1",
"transcript_support_level": null,
"aa_start": 393,
"aa_end": null,
"aa_length": 544,
"cds_start": 1177,
"cds_end": null,
"cds_length": 1635,
"cdna_start": 1551,
"cdna_end": null,
"cdna_length": 3328,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.1177G>A",
"hgvs_p": "p.Glu393Lys",
"transcript": "NM_001243249.2",
"protein_id": "NP_001230178.1",
"transcript_support_level": null,
"aa_start": 393,
"aa_end": null,
"aa_length": 544,
"cds_start": 1177,
"cds_end": null,
"cds_length": 1635,
"cdna_start": 1583,
"cdna_end": null,
"cdna_length": 3360,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.1018G>A",
"hgvs_p": "p.Glu340Lys",
"transcript": "NM_001243247.2",
"protein_id": "NP_001230176.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 491,
"cds_start": 1018,
"cds_end": null,
"cds_length": 1476,
"cdna_start": 1488,
"cdna_end": null,
"cdna_length": 3265,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.715G>A",
"hgvs_p": "p.Glu239Lys",
"transcript": "NM_001039476.3",
"protein_id": "NP_001034565.1",
"transcript_support_level": null,
"aa_start": 239,
"aa_end": null,
"aa_length": 390,
"cds_start": 715,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 1453,
"cdna_end": null,
"cdna_length": 3230,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "n.1275G>A",
"hgvs_p": null,
"transcript": "ENST00000610509.1",
"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": 2917,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "n.*888G>A",
"hgvs_p": null,
"transcript": "ENST00000622194.4",
"protein_id": "ENSP00000478045.1",
"transcript_support_level": 5,
"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": 2981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "n.*888G>A",
"hgvs_p": null,
"transcript": "ENST00000622194.4",
"protein_id": "ENSP00000478045.1",
"transcript_support_level": 5,
"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": 2981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"dbsnp": "rs547498080",
"frequency_reference_population": 0.00014432278,
"hom_count_reference_population": 0,
"allele_count_reference_population": 230,
"gnomad_exomes_af": 0.000154706,
"gnomad_genomes_af": 0.0000459915,
"gnomad_exomes_ac": 223,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.40861549973487854,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.273,
"revel_prediction": "Benign",
"alphamissense_score": 0.0802,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.655,
"phylop100way_prediction": "Uncertain_significance",
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BP6,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000611875.5",
"gene_symbol": "NPRL3",
"hgnc_id": 14124,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Glu418Lys"
}
],
"clinvar_disease": " familial focal, with variable foci 3,Epilepsy,Inborn genetic diseases,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:2",
"phenotype_combined": "Epilepsy, familial focal, with variable foci 3|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}