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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: 3-25729184-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=25729184&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 25729184,
"ref": "G",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000280700.10",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1560C>A",
"hgvs_p": "p.Gly520Gly",
"transcript": "NM_018297.4",
"protein_id": "NP_060767.2",
"transcript_support_level": null,
"aa_start": 520,
"aa_end": null,
"aa_length": 654,
"cds_start": 1560,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1613,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": "ENST00000280700.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1560C>A",
"hgvs_p": "p.Gly520Gly",
"transcript": "ENST00000280700.10",
"protein_id": "ENSP00000280700.5",
"transcript_support_level": 1,
"aa_start": 520,
"aa_end": null,
"aa_length": 654,
"cds_start": 1560,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1613,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": "NM_018297.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1506C>A",
"hgvs_p": "p.Gly502Gly",
"transcript": "ENST00000428257.5",
"protein_id": "ENSP00000387430.1",
"transcript_support_level": 1,
"aa_start": 502,
"aa_end": null,
"aa_length": 636,
"cds_start": 1506,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 1614,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1497C>A",
"hgvs_p": "p.Gly499Gly",
"transcript": "ENST00000308710.9",
"protein_id": "ENSP00000307980.5",
"transcript_support_level": 1,
"aa_start": 499,
"aa_end": null,
"aa_length": 633,
"cds_start": 1497,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 1497,
"cdna_end": null,
"cdna_length": 2086,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1560C>A",
"hgvs_p": "p.Gly520Gly",
"transcript": "ENST00000396649.7",
"protein_id": "ENSP00000379886.3",
"transcript_support_level": 1,
"aa_start": 520,
"aa_end": null,
"aa_length": 558,
"cds_start": 1560,
"cds_end": null,
"cds_length": 1677,
"cdna_start": 1608,
"cdna_end": null,
"cdna_length": 2024,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.1367C>A",
"hgvs_p": null,
"transcript": "ENST00000489271.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2288,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1530C>A",
"hgvs_p": "p.Gly510Gly",
"transcript": "ENST00000676225.1",
"protein_id": "ENSP00000501622.1",
"transcript_support_level": null,
"aa_start": 510,
"aa_end": null,
"aa_length": 644,
"cds_start": 1530,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 1564,
"cdna_end": null,
"cdna_length": 2253,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1506C>A",
"hgvs_p": "p.Gly502Gly",
"transcript": "NM_001145293.2",
"protein_id": "NP_001138765.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 636,
"cds_start": 1506,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 1559,
"cdna_end": null,
"cdna_length": 2480,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1434C>A",
"hgvs_p": "p.Gly478Gly",
"transcript": "NM_001145294.2",
"protein_id": "NP_001138766.1",
"transcript_support_level": null,
"aa_start": 478,
"aa_end": null,
"aa_length": 612,
"cds_start": 1434,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1608,
"cdna_end": null,
"cdna_length": 2529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1434C>A",
"hgvs_p": "p.Gly478Gly",
"transcript": "ENST00000417874.6",
"protein_id": "ENSP00000389888.2",
"transcript_support_level": 2,
"aa_start": 478,
"aa_end": null,
"aa_length": 612,
"cds_start": 1434,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1608,
"cdna_end": null,
"cdna_length": 2062,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1560C>A",
"hgvs_p": "p.Gly520Gly",
"transcript": "NM_001145295.2",
"protein_id": "NP_001138767.1",
"transcript_support_level": null,
"aa_start": 520,
"aa_end": null,
"aa_length": 558,
"cds_start": 1560,
"cds_end": null,
"cds_length": 1677,
"cdna_start": 1613,
"cdna_end": null,
"cdna_length": 2356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.873C>A",
"hgvs_p": "p.Gly291Gly",
"transcript": "ENST00000675680.1",
"protein_id": "ENSP00000502709.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 425,
"cds_start": 873,
"cds_end": null,
"cds_length": 1278,
"cdna_start": 874,
"cdna_end": null,
"cdna_length": 1464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1395C>A",
"hgvs_p": "p.Gly465Gly",
"transcript": "XM_005265316.1",
"protein_id": "XP_005265373.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 599,
"cds_start": 1395,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1448,
"cdna_end": null,
"cdna_length": 2369,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1560C>A",
"hgvs_p": "p.Gly520Gly",
"transcript": "XM_017006839.3",
"protein_id": "XP_016862328.1",
"transcript_support_level": null,
"aa_start": 520,
"aa_end": null,
"aa_length": 591,
"cds_start": 1560,
"cds_end": null,
"cds_length": 1776,
"cdna_start": 1613,
"cdna_end": null,
"cdna_length": 1887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1341C>A",
"hgvs_p": "p.Gly447Gly",
"transcript": "XM_047448556.1",
"protein_id": "XP_047304512.1",
"transcript_support_level": null,
"aa_start": 447,
"aa_end": null,
"aa_length": 581,
"cds_start": 1341,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 1394,
"cdna_end": null,
"cdna_length": 2315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1329C>A",
"hgvs_p": "p.Gly443Gly",
"transcript": "XM_011533944.1",
"protein_id": "XP_011532246.1",
"transcript_support_level": null,
"aa_start": 443,
"aa_end": null,
"aa_length": 577,
"cds_start": 1329,
"cds_end": null,
"cds_length": 1734,
"cdna_start": 1564,
"cdna_end": null,
"cdna_length": 2485,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1506C>A",
"hgvs_p": "p.Gly502Gly",
"transcript": "XM_047448557.1",
"protein_id": "XP_047304513.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 540,
"cds_start": 1506,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1559,
"cdna_end": null,
"cdna_length": 2302,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1395C>A",
"hgvs_p": "p.Gly465Gly",
"transcript": "XM_005265317.1",
"protein_id": "XP_005265374.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 503,
"cds_start": 1395,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 1448,
"cdna_end": null,
"cdna_length": 2191,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1341C>A",
"hgvs_p": "p.Gly447Gly",
"transcript": "XM_047448558.1",
"protein_id": "XP_047304514.1",
"transcript_support_level": null,
"aa_start": 447,
"aa_end": null,
"aa_length": 485,
"cds_start": 1341,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 1394,
"cdna_end": null,
"cdna_length": 2137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.*590C>A",
"hgvs_p": null,
"transcript": "ENST00000280699.13",
"protein_id": "ENSP00000280699.9",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.*1651C>A",
"hgvs_p": null,
"transcript": "ENST00000463611.2",
"protein_id": "ENSP00000501918.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.248C>A",
"hgvs_p": null,
"transcript": "ENST00000467224.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.2463C>A",
"hgvs_p": null,
"transcript": "ENST00000493324.5",
"protein_id": null,
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"aa_start": null,
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}
],
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"computational_prediction_selected": "Benign",
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"splice_prediction_selected": "Benign",
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"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
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"phylop100way_prediction": "Benign",
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"spliceai_max_prediction": "Benign",
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{
"score": -3,
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"pathogenic_score": 2,
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"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
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],
"inheritance_mode": "AR",
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],
"clinvar_disease": "Congenital disorder of deglycosylation",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Congenital disorder of deglycosylation",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}