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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: 16-15696736-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=15696736&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 15696736,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_017668.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "NM_017668.3",
"protein_id": "NP_060138.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000396354.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017668.3"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "ENST00000396354.6",
"protein_id": "ENSP00000379642.1",
"transcript_support_level": 1,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017668.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396354.6"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "ENST00000396355.5",
"protein_id": "ENSP00000379643.1",
"transcript_support_level": 1,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396355.5"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "NM_001143979.2",
"protein_id": "NP_001137451.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001143979.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "ENST00000911227.1",
"protein_id": "ENSP00000581286.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911227.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "ENST00000911228.1",
"protein_id": "ENSP00000581287.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911228.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "ENST00000911231.1",
"protein_id": "ENSP00000581290.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911231.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "ENST00000911233.1",
"protein_id": "ENSP00000581292.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911233.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "ENST00000911234.1",
"protein_id": "ENSP00000581293.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911234.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "ENST00000963926.1",
"protein_id": "ENSP00000633985.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963926.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "ENST00000963928.1",
"protein_id": "ENSP00000633987.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963928.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp",
"transcript": "ENST00000963929.1",
"protein_id": "ENSP00000633988.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 335,
"cds_start": 823,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963929.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.820C>T",
"hgvs_p": "p.Arg274Trp",
"transcript": "ENST00000911229.1",
"protein_id": "ENSP00000581288.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 334,
"cds_start": 820,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911229.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.820C>T",
"hgvs_p": "p.Arg274Trp",
"transcript": "ENST00000911232.1",
"protein_id": "ENSP00000581291.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 334,
"cds_start": 820,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911232.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.820C>T",
"hgvs_p": "p.Arg274Trp",
"transcript": "ENST00000934469.1",
"protein_id": "ENSP00000604528.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 334,
"cds_start": 820,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934469.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"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": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.731C>T",
"hgvs_p": "p.Pro244Leu",
"transcript": "ENST00000674581.1",
"protein_id": "ENSP00000502100.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 282,
"cds_start": 731,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674581.1"
},
{
"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": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.643C>T",
"hgvs_p": "p.Arg215Trp",
"transcript": "ENST00000911230.1",
"protein_id": "ENSP00000581289.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 275,
"cds_start": 643,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911230.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.520C>T",
"hgvs_p": "p.Arg174Trp",
"transcript": "ENST00000963927.1",
"protein_id": "ENSP00000633986.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 234,
"cds_start": 520,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963927.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.385C>T",
"hgvs_p": "p.Arg129Trp",
"transcript": "ENST00000574109.5",
"protein_id": "ENSP00000459875.1",
"transcript_support_level": 3,
"aa_start": 129,
"aa_end": null,
"aa_length": 173,
"cds_start": 385,
"cds_end": null,
"cds_length": 522,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000574109.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.244C>T",
"hgvs_p": "p.Arg82Trp",
"transcript": "ENST00000576502.5",
"protein_id": "ENSP00000461748.1",
"transcript_support_level": 2,
"aa_start": 82,
"aa_end": null,
"aa_length": 153,
"cds_start": 244,
"cds_end": null,
"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000576502.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.202C>T",
"hgvs_p": "p.Arg68Trp",
"transcript": "ENST00000572967.1",
"protein_id": "ENSP00000459918.1",
"transcript_support_level": 3,
"aa_start": 68,
"aa_end": null,
"aa_length": 139,
"cds_start": 202,
"cds_end": null,
"cds_length": 420,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000572967.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDE1",
"gene_hgnc_id": 17619,
"hgvs_c": "c.919C>T",
"hgvs_p": "p.Arg307Trp",
"transcript": "XM_006720897.5",
"protein_id": "XP_006720960.1",
"transcript_support_level": null,
"aa_start": 307,
"aa_end": null,
"aa_length": 379,
"cds_start": 919,
"cds_end": null,
"cds_length": 1140,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
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],
"gene_symbol": "NDE1",
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"dbsnp": "rs769264617",
"frequency_reference_population": 0.000008673704,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000889261,
"gnomad_genomes_af": 0.00000657091,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9468445181846619,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.328,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.6857,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.1,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.374,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_017668.3",
"gene_symbol": "NDE1",
"hgnc_id": 17619,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275Trp"
}
],
"clinvar_disease": "Inborn genetic diseases,Lissencephaly 4,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Lissencephaly 4|Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}