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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: X-71169903-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=71169903&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"BP4",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NLGN3",
"hgnc_id": 14289,
"hgvs_c": "c.2353C>T",
"hgvs_p": "p.Arg785Cys",
"inheritance_mode": "XL,Unknown",
"pathogenic_score": 0,
"score": -5,
"transcript": "NM_181303.2",
"verdict": "Likely_benign"
},
{
"benign_score": 5,
"criteria": [
"BP4",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000228427",
"hgnc_id": null,
"hgvs_c": "n.346+14008G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -5,
"transcript": "ENST00000740246.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS2",
"acmg_score": -5,
"allele_count_reference_population": 20,
"alphamissense_prediction": null,
"alphamissense_score": 0.1207,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.04,
"chr": "X",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.3780382573604584,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 848,
"aa_ref": "R",
"aa_start": 785,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3975,
"cdna_start": 2677,
"cds_end": null,
"cds_length": 2547,
"cds_start": 2353,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_181303.2",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2353C>T",
"hgvs_p": "p.Arg785Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000358741.4",
"protein_coding": true,
"protein_id": "NP_851820.1",
"strand": true,
"transcript": "NM_181303.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 848,
"aa_ref": "R",
"aa_start": 785,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3975,
"cdna_start": 2677,
"cds_end": null,
"cds_length": 2547,
"cds_start": 2353,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000358741.4",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2353C>T",
"hgvs_p": "p.Arg785Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_181303.2",
"protein_coding": true,
"protein_id": "ENSP00000351591.4",
"strand": true,
"transcript": "ENST00000358741.4",
"transcript_support_level": 5
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 828,
"aa_ref": "R",
"aa_start": 765,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3913,
"cdna_start": 2615,
"cds_end": null,
"cds_length": 2487,
"cds_start": 2293,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000374051.7",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2293C>T",
"hgvs_p": "p.Arg765Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000363163.3",
"strand": true,
"transcript": "ENST00000374051.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3789,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000476589.2",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "n.2532C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000476589.2",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 4125,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000685718.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "n.*1700C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000510514.1",
"strand": true,
"transcript": "ENST00000685718.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 4125,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000685718.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "n.*1700C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000510514.1",
"strand": true,
"transcript": "ENST00000685718.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 848,
"aa_ref": "R",
"aa_start": 785,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4423,
"cdna_start": 3125,
"cds_end": null,
"cds_length": 2547,
"cds_start": 2353,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000904687.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2353C>T",
"hgvs_p": "p.Arg785Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574746.1",
"strand": true,
"transcript": "ENST00000904687.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 848,
"aa_ref": "R",
"aa_start": 785,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4508,
"cdna_start": 3212,
"cds_end": null,
"cds_length": 2547,
"cds_start": 2353,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000957026.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2353C>T",
"hgvs_p": "p.Arg785Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627085.1",
"strand": true,
"transcript": "ENST00000957026.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 828,
"aa_ref": "R",
"aa_start": 765,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3915,
"cdna_start": 2617,
"cds_end": null,
"cds_length": 2487,
"cds_start": 2293,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_018977.4",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2293C>T",
"hgvs_p": "p.Arg765Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_061850.2",
"strand": true,
"transcript": "NM_018977.4",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 828,
"aa_ref": "R",
"aa_start": 765,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3913,
"cdna_start": 2615,
"cds_end": null,
"cds_length": 2487,
"cds_start": 2293,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000939110.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2293C>T",
"hgvs_p": "p.Arg765Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000609169.1",
"strand": true,
"transcript": "ENST00000939110.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 817,
"aa_ref": "R",
"aa_start": 754,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3885,
"cdna_start": 2587,
"cds_end": null,
"cds_length": 2454,
"cds_start": 2260,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000939109.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2260C>T",
"hgvs_p": "p.Arg754Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000609168.1",
"strand": true,
"transcript": "ENST00000939109.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 808,
"aa_ref": "R",
"aa_start": 745,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3855,
"cdna_start": 2557,
"cds_end": null,
"cds_length": 2427,
"cds_start": 2233,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001166660.2",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2233C>T",
"hgvs_p": "p.Arg745Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001160132.1",
"strand": true,
"transcript": "NM_001166660.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 808,
"aa_ref": "R",
"aa_start": 745,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3812,
"cdna_start": 2555,
"cds_end": null,
"cds_length": 2427,
"cds_start": 2233,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000536169.6",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2233C>T",
"hgvs_p": "p.Arg745Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000445298.1",
"strand": true,
"transcript": "ENST00000536169.6",
"transcript_support_level": 5
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 808,
"aa_ref": "R",
"aa_start": 745,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3824,
"cdna_start": 2526,
"cds_end": null,
"cds_length": 2427,
"cds_start": 2233,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000939108.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2233C>T",
"hgvs_p": "p.Arg745Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000609167.1",
"strand": true,
"transcript": "ENST00000939108.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 758,
"aa_ref": "R",
"aa_start": 695,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3670,
"cdna_start": 2427,
"cds_end": null,
"cds_length": 2277,
"cds_start": 2083,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000689857.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2083C>T",
"hgvs_p": "p.Arg695Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510719.1",
"strand": true,
"transcript": "ENST00000689857.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 735,
"aa_ref": "R",
"aa_start": 672,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3512,
"cdna_start": 2358,
"cds_end": null,
"cds_length": 2208,
"cds_start": 2014,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000689968.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2014C>T",
"hgvs_p": "p.Arg672Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510150.1",
"strand": true,
"transcript": "ENST00000689968.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 731,
"aa_ref": "R",
"aa_start": 668,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3462,
"cdna_start": 2164,
"cds_end": null,
"cds_length": 2196,
"cds_start": 2002,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001437941.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2002C>T",
"hgvs_p": "p.Arg668Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001424870.1",
"strand": true,
"transcript": "NM_001437941.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 731,
"aa_ref": "R",
"aa_start": 668,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3540,
"cdna_start": 2242,
"cds_end": null,
"cds_length": 2196,
"cds_start": 2002,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001438296.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2002C>T",
"hgvs_p": "p.Arg668Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001425225.1",
"strand": true,
"transcript": "NM_001438296.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 731,
"aa_ref": "R",
"aa_start": 668,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3494,
"cdna_start": 2237,
"cds_end": null,
"cds_length": 2196,
"cds_start": 2002,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000687220.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2002C>T",
"hgvs_p": "p.Arg668Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509531.1",
"strand": true,
"transcript": "ENST00000687220.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 731,
"aa_ref": "R",
"aa_start": 668,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3419,
"cdna_start": 2162,
"cds_end": null,
"cds_length": 2196,
"cds_start": 2002,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000688566.1",
"gene_hgnc_id": 14289,
"gene_symbol": "NLGN3",
"hgvs_c": "c.2002C>T",
"hgvs_p": "p.Arg668Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509202.1",
"strand": true,
"transcript": "ENST00000688566.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 711,
"aa_ref": "R",
"aa_start": 648,
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