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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: 3-25729236-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=25729236&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 16,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NGLY1",
"hgnc_id": 17646,
"hgvs_c": "c.1508G>A",
"hgvs_p": "p.Arg503His",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -16,
"transcript": "NM_018297.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1",
"acmg_score": -16,
"allele_count_reference_population": 414,
"alphamissense_prediction": null,
"alphamissense_score": 0.0545,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.75,
"chr": "3",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Congenital disorder of deglycosylation,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0040923357009887695,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 654,
"aa_ref": "R",
"aa_start": 503,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2534,
"cdna_start": 1561,
"cds_end": null,
"cds_length": 1965,
"cds_start": 1508,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_018297.4",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1508G>A",
"hgvs_p": "p.Arg503His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000280700.10",
"protein_coding": true,
"protein_id": "NP_060767.2",
"strand": false,
"transcript": "NM_018297.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 654,
"aa_ref": "R",
"aa_start": 503,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2534,
"cdna_start": 1561,
"cds_end": null,
"cds_length": 1965,
"cds_start": 1508,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000280700.10",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1508G>A",
"hgvs_p": "p.Arg503His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018297.4",
"protein_coding": true,
"protein_id": "ENSP00000280700.5",
"strand": false,
"transcript": "ENST00000280700.10",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 636,
"aa_ref": "R",
"aa_start": 485,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2534,
"cdna_start": 1562,
"cds_end": null,
"cds_length": 1911,
"cds_start": 1454,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000428257.5",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1454G>A",
"hgvs_p": "p.Arg485His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000387430.1",
"strand": false,
"transcript": "ENST00000428257.5",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 633,
"aa_ref": "R",
"aa_start": 482,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2086,
"cdna_start": 1445,
"cds_end": null,
"cds_length": 1902,
"cds_start": 1445,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000308710.9",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1445G>A",
"hgvs_p": "p.Arg482His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000307980.5",
"strand": false,
"transcript": "ENST00000308710.9",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 558,
"aa_ref": "R",
"aa_start": 503,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2024,
"cdna_start": 1556,
"cds_end": null,
"cds_length": 1677,
"cds_start": 1508,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000396649.7",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1508G>A",
"hgvs_p": "p.Arg503His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000379886.3",
"strand": false,
"transcript": "ENST00000396649.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2288,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000489271.5",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "n.1315G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000489271.5",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 684,
"aa_ref": "R",
"aa_start": 533,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2293,
"cdna_start": 1651,
"cds_end": null,
"cds_length": 2055,
"cds_start": 1598,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000877204.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1598G>A",
"hgvs_p": "p.Arg533His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547263.1",
"strand": false,
"transcript": "ENST00000877204.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 682,
"aa_ref": "R",
"aa_start": 531,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2249,
"cdna_start": 1603,
"cds_end": null,
"cds_length": 2049,
"cds_start": 1592,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000877207.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1592G>A",
"hgvs_p": "p.Arg531His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547266.1",
"strand": false,
"transcript": "ENST00000877207.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 673,
"aa_ref": "R",
"aa_start": 522,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2313,
"cdna_start": 1666,
"cds_end": null,
"cds_length": 2022,
"cds_start": 1565,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000942732.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1565G>A",
"hgvs_p": "p.Arg522His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612791.1",
"strand": false,
"transcript": "ENST00000942732.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 671,
"aa_ref": "R",
"aa_start": 520,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2580,
"cdna_start": 1610,
"cds_end": null,
"cds_length": 2016,
"cds_start": 1559,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000942731.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1559G>A",
"hgvs_p": "p.Arg520His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612790.1",
"strand": false,
"transcript": "ENST00000942731.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 655,
"aa_ref": "R",
"aa_start": 504,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2225,
"cdna_start": 1563,
"cds_end": null,
"cds_length": 1968,
"cds_start": 1511,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000942734.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1511G>A",
"hgvs_p": "p.Arg504His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612793.1",
"strand": false,
"transcript": "ENST00000942734.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 654,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2534,
"cdna_start": 1561,
"cds_end": null,
"cds_length": 1965,
"cds_start": 1508,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000942730.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1508G>A",
"hgvs_p": "p.Arg503His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612789.1",
"strand": false,
"transcript": "ENST00000942730.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
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"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2163,
"cdna_start": 1529,
"cds_end": null,
"cds_length": 1962,
"cds_start": 1505,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000942736.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1505G>A",
"hgvs_p": "p.Arg502His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612795.1",
"strand": false,
"transcript": "ENST00000942736.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 646,
"aa_ref": "R",
"aa_start": 495,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2160,
"cdna_start": 1538,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1484,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000877206.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1484G>A",
"hgvs_p": "p.Arg495His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547265.1",
"strand": false,
"transcript": "ENST00000877206.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 644,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2253,
"cdna_start": 1512,
"cds_end": null,
"cds_length": 1935,
"cds_start": 1478,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000676225.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1478G>A",
"hgvs_p": "p.Arg493His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501622.1",
"strand": false,
"transcript": "ENST00000676225.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 638,
"aa_ref": "R",
"aa_start": 487,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2177,
"cdna_start": 1513,
"cds_end": null,
"cds_length": 1917,
"cds_start": 1460,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000942733.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1460G>A",
"hgvs_p": "p.Arg487His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612792.1",
"strand": false,
"transcript": "ENST00000942733.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 636,
"aa_ref": "R",
"aa_start": 485,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2480,
"cdna_start": 1507,
"cds_end": null,
"cds_length": 1911,
"cds_start": 1454,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001145293.2",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1454G>A",
"hgvs_p": "p.Arg485His",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001138765.1",
"strand": false,
"transcript": "NM_001145293.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
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"aa_length": 627,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2124,
"cdna_start": 1482,
"cds_end": null,
"cds_length": 1884,
"cds_start": 1427,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000877203.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1427G>A",
"hgvs_p": "p.Arg476His",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547262.1",
"strand": false,
"transcript": "ENST00000877203.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
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"aa_length": 612,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2529,
"cdna_start": 1556,
"cds_end": null,
"cds_length": 1839,
"cds_start": 1382,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001145294.2",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1382G>A",
"hgvs_p": "p.Arg461His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001138766.1",
"strand": false,
"transcript": "NM_001145294.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 612,
"aa_ref": "R",
"aa_start": 461,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2062,
"cdna_start": 1556,
"cds_end": null,
"cds_length": 1839,
"cds_start": 1382,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000417874.6",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
"hgvs_c": "c.1382G>A",
"hgvs_p": "p.Arg461His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000389888.2",
"strand": false,
"transcript": "ENST00000417874.6",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 599,
"aa_ref": "R",
"aa_start": 448,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2632,
"cdna_start": 1432,
"cds_end": null,
"cds_length": 1800,
"cds_start": 1343,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000877202.1",
"gene_hgnc_id": 17646,
"gene_symbol": "NGLY1",
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}