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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: 9-131127590-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=131127590&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 131127590,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005085.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "NM_005085.4",
"protein_id": "NP_005076.3",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2090,
"cds_start": 112,
"cds_end": null,
"cds_length": 6273,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000359428.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005085.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000359428.10",
"protein_id": "ENSP00000352400.5",
"transcript_support_level": 1,
"aa_start": 38,
"aa_end": null,
"aa_length": 2090,
"cds_start": 112,
"cds_end": null,
"cds_length": 6273,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005085.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000359428.10"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000411637.6",
"protein_id": "ENSP00000396576.2",
"transcript_support_level": 1,
"aa_start": 38,
"aa_end": null,
"aa_length": 2080,
"cds_start": 112,
"cds_end": null,
"cds_length": 6243,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000411637.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.-159C>T",
"hgvs_p": null,
"transcript": "ENST00000651639.1",
"protein_id": "ENSP00000498545.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 186,
"cds_start": null,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000651639.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.-159C>T",
"hgvs_p": null,
"transcript": "ENST00000531584.1",
"protein_id": "ENSP00000435874.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 51,
"cds_start": null,
"cds_end": null,
"cds_length": 156,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000531584.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000897205.1",
"protein_id": "ENSP00000567264.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2091,
"cds_start": 112,
"cds_end": null,
"cds_length": 6276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897205.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "NM_001318324.2",
"protein_id": "NP_001305253.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2080,
"cds_start": 112,
"cds_end": null,
"cds_length": 6243,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318324.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000897208.1",
"protein_id": "ENSP00000567267.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2079,
"cds_start": 112,
"cds_end": null,
"cds_length": 6240,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897208.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000897209.1",
"protein_id": "ENSP00000567268.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2079,
"cds_start": 112,
"cds_end": null,
"cds_length": 6240,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897209.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000652454.1",
"protein_id": "ENSP00000499001.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2078,
"cds_start": 112,
"cds_end": null,
"cds_length": 6237,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000652454.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000922158.1",
"protein_id": "ENSP00000592217.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2042,
"cds_start": 112,
"cds_end": null,
"cds_length": 6129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922158.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000897206.1",
"protein_id": "ENSP00000567265.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2041,
"cds_start": 112,
"cds_end": null,
"cds_length": 6126,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897206.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000922160.1",
"protein_id": "ENSP00000592219.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2030,
"cds_start": 112,
"cds_end": null,
"cds_length": 6093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922160.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000922161.1",
"protein_id": "ENSP00000592220.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2029,
"cds_start": 112,
"cds_end": null,
"cds_length": 6090,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922161.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000922162.1",
"protein_id": "ENSP00000592221.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2011,
"cds_start": 112,
"cds_end": null,
"cds_length": 6036,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922162.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000897207.1",
"protein_id": "ENSP00000567266.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 2010,
"cds_start": 112,
"cds_end": null,
"cds_length": 6033,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897207.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000897210.1",
"protein_id": "ENSP00000567269.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 1984,
"cds_start": 112,
"cds_end": null,
"cds_length": 5955,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897210.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000922159.1",
"protein_id": "ENSP00000592218.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 1956,
"cds_start": 112,
"cds_end": null,
"cds_length": 5871,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922159.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000922164.1",
"protein_id": "ENSP00000592223.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 1951,
"cds_start": 112,
"cds_end": null,
"cds_length": 5856,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922164.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000922163.1",
"protein_id": "ENSP00000592222.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 1945,
"cds_start": 112,
"cds_end": null,
"cds_length": 5838,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922163.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.112C>T",
"hgvs_p": "p.Arg38Cys",
"transcript": "ENST00000922165.1",
"protein_id": "ENSP00000592224.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 1940,
"cds_start": 112,
"cds_end": null,
"cds_length": 5823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922165.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP214",
"gene_hgnc_id": 8064,
"hgvs_c": "c.76C>T",
"hgvs_p": "p.Arg26Cys",
"transcript": "ENST00000651022.1",
"protein_id": "ENSP00000498226.1",
"transcript_support_level": null,
"aa_start": 26,
"aa_end": null,
"aa_length": 718,
"cds_start": 76,
"cds_end": null,
"cds_length": 2158,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
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"computational_prediction_selected": "Pathogenic",
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"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"revel_prediction": "Pathogenic",
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"bayesdelnoaf_score": 0.33,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.06,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
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"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 11,
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"criteria": [
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"verdict": "Pathogenic",
"transcript": "NM_005085.4",
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"effects": [
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"inheritance_mode": "AR",
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],
"clinvar_disease": " 9, acute, infection-induced, susceptibility to,Encephalopathy,Progressive microcephaly,Recurrent encephalopathy",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Progressive microcephaly;Recurrent encephalopathy|Encephalopathy, acute, infection-induced, susceptibility to, 9",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}