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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: 3-136928099-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=136928099&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 136928099,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_006153.6",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "NM_001291999.2",
"protein_id": "NP_001278928.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000481752.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291999.2"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000481752.6",
"protein_id": "ENSP00000417273.1",
"transcript_support_level": 5,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001291999.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000481752.6"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000288986.6",
"protein_id": "ENSP00000288986.2",
"transcript_support_level": 1,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000288986.6"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000951211.1",
"protein_id": "ENSP00000621270.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 438,
"cds_start": 98,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951211.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000951212.1",
"protein_id": "ENSP00000621271.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 408,
"cds_start": 98,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951212.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "NM_006153.6",
"protein_id": "NP_006144.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006153.6"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000898712.1",
"protein_id": "ENSP00000568771.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898712.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000898713.1",
"protein_id": "ENSP00000568772.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898713.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000898714.1",
"protein_id": "ENSP00000568773.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898714.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000898715.1",
"protein_id": "ENSP00000568774.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898715.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000898716.1",
"protein_id": "ENSP00000568775.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898716.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000898717.1",
"protein_id": "ENSP00000568776.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898717.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000898718.1",
"protein_id": "ENSP00000568777.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898718.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000898719.1",
"protein_id": "ENSP00000568778.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898719.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000898720.1",
"protein_id": "ENSP00000568779.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898720.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000898721.1",
"protein_id": "ENSP00000568780.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898721.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000938741.1",
"protein_id": "ENSP00000608800.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938741.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000951209.1",
"protein_id": "ENSP00000621268.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951209.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000951210.1",
"protein_id": "ENSP00000621269.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951210.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000951213.1",
"protein_id": "ENSP00000621272.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951213.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000951214.1",
"protein_id": "ENSP00000621273.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951214.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"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": "NCK1",
"gene_hgnc_id": 7664,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Asp33Gly",
"transcript": "ENST00000951215.1",
"protein_id": "ENSP00000621274.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 377,
"cds_start": 98,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951215.1"
},
{
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],
"gene_symbol": "NCK1",
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"frequency_reference_population": 6.84061e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
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"gnomad_exomes_homalt": 0,
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"computational_score_selected": 0.8119043111801147,
"computational_prediction_selected": "Pathogenic",
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"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.582,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9931,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.947,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"apogee2_score": null,
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"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
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"pathogenic_score": 3,
"criteria": [
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"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006153.6",
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"effects": [
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],
"inheritance_mode": "AD",
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],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}