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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: 3-25733897-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=25733897&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 25733897,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_018297.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1235A>G",
"hgvs_p": "p.Asp412Gly",
"transcript": "NM_018297.4",
"protein_id": "NP_060767.2",
"transcript_support_level": null,
"aa_start": 412,
"aa_end": null,
"aa_length": 654,
"cds_start": 1235,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1288,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": "ENST00000280700.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018297.4"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1235A>G",
"hgvs_p": "p.Asp412Gly",
"transcript": "ENST00000280700.10",
"protein_id": "ENSP00000280700.5",
"transcript_support_level": 1,
"aa_start": 412,
"aa_end": null,
"aa_length": 654,
"cds_start": 1235,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1288,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": "NM_018297.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000280700.10"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1181A>G",
"hgvs_p": "p.Asp394Gly",
"transcript": "ENST00000428257.5",
"protein_id": "ENSP00000387430.1",
"transcript_support_level": 1,
"aa_start": 394,
"aa_end": null,
"aa_length": 636,
"cds_start": 1181,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 1289,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000428257.5"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1172A>G",
"hgvs_p": "p.Asp391Gly",
"transcript": "ENST00000308710.9",
"protein_id": "ENSP00000307980.5",
"transcript_support_level": 1,
"aa_start": 391,
"aa_end": null,
"aa_length": 633,
"cds_start": 1172,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 1172,
"cdna_end": null,
"cdna_length": 2086,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000308710.9"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1235A>G",
"hgvs_p": "p.Asp412Gly",
"transcript": "ENST00000396649.7",
"protein_id": "ENSP00000379886.3",
"transcript_support_level": 1,
"aa_start": 412,
"aa_end": null,
"aa_length": 558,
"cds_start": 1235,
"cds_end": null,
"cds_length": 1677,
"cdna_start": 1283,
"cdna_end": null,
"cdna_length": 2024,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396649.7"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1325A>G",
"hgvs_p": "p.Asp442Gly",
"transcript": "ENST00000877204.1",
"protein_id": "ENSP00000547263.1",
"transcript_support_level": null,
"aa_start": 442,
"aa_end": null,
"aa_length": 684,
"cds_start": 1325,
"cds_end": null,
"cds_length": 2055,
"cdna_start": 1378,
"cdna_end": null,
"cdna_length": 2293,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877204.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1319A>G",
"hgvs_p": "p.Asp440Gly",
"transcript": "ENST00000877207.1",
"protein_id": "ENSP00000547266.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 682,
"cds_start": 1319,
"cds_end": null,
"cds_length": 2049,
"cdna_start": 1330,
"cdna_end": null,
"cdna_length": 2249,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877207.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1292A>G",
"hgvs_p": "p.Asp431Gly",
"transcript": "ENST00000942732.1",
"protein_id": "ENSP00000612791.1",
"transcript_support_level": null,
"aa_start": 431,
"aa_end": null,
"aa_length": 673,
"cds_start": 1292,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 1393,
"cdna_end": null,
"cdna_length": 2313,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942732.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1286A>G",
"hgvs_p": "p.Asp429Gly",
"transcript": "ENST00000942731.1",
"protein_id": "ENSP00000612790.1",
"transcript_support_level": null,
"aa_start": 429,
"aa_end": null,
"aa_length": 671,
"cds_start": 1286,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 1337,
"cdna_end": null,
"cdna_length": 2580,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942731.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1238A>G",
"hgvs_p": "p.Asp413Gly",
"transcript": "ENST00000942734.1",
"protein_id": "ENSP00000612793.1",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 655,
"cds_start": 1238,
"cds_end": null,
"cds_length": 1968,
"cdna_start": 1290,
"cdna_end": null,
"cdna_length": 2225,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942734.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1235A>G",
"hgvs_p": "p.Asp412Gly",
"transcript": "ENST00000942730.1",
"protein_id": "ENSP00000612789.1",
"transcript_support_level": null,
"aa_start": 412,
"aa_end": null,
"aa_length": 654,
"cds_start": 1235,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1288,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942730.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1232A>G",
"hgvs_p": "p.Asp411Gly",
"transcript": "ENST00000942736.1",
"protein_id": "ENSP00000612795.1",
"transcript_support_level": null,
"aa_start": 411,
"aa_end": null,
"aa_length": 653,
"cds_start": 1232,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 1256,
"cdna_end": null,
"cdna_length": 2163,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942736.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1211A>G",
"hgvs_p": "p.Asp404Gly",
"transcript": "ENST00000877206.1",
"protein_id": "ENSP00000547265.1",
"transcript_support_level": null,
"aa_start": 404,
"aa_end": null,
"aa_length": 646,
"cds_start": 1211,
"cds_end": null,
"cds_length": 1941,
"cdna_start": 1265,
"cdna_end": null,
"cdna_length": 2160,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877206.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1205A>G",
"hgvs_p": "p.Asp402Gly",
"transcript": "ENST00000676225.1",
"protein_id": "ENSP00000501622.1",
"transcript_support_level": null,
"aa_start": 402,
"aa_end": null,
"aa_length": 644,
"cds_start": 1205,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 1239,
"cdna_end": null,
"cdna_length": 2253,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676225.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1181A>G",
"hgvs_p": "p.Asp394Gly",
"transcript": "NM_001145293.2",
"protein_id": "NP_001138765.1",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 636,
"cds_start": 1181,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 1234,
"cdna_end": null,
"cdna_length": 2480,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145293.2"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1319A>G",
"hgvs_p": "p.Asp440Gly",
"transcript": "ENST00000877203.1",
"protein_id": "ENSP00000547262.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 627,
"cds_start": 1319,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 1374,
"cdna_end": null,
"cdna_length": 2124,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877203.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1109A>G",
"hgvs_p": "p.Asp370Gly",
"transcript": "NM_001145294.2",
"protein_id": "NP_001138766.1",
"transcript_support_level": null,
"aa_start": 370,
"aa_end": null,
"aa_length": 612,
"cds_start": 1109,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1283,
"cdna_end": null,
"cdna_length": 2529,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145294.2"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1109A>G",
"hgvs_p": "p.Asp370Gly",
"transcript": "ENST00000417874.6",
"protein_id": "ENSP00000389888.2",
"transcript_support_level": 2,
"aa_start": 370,
"aa_end": null,
"aa_length": 612,
"cds_start": 1109,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1283,
"cdna_end": null,
"cdna_length": 2062,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000417874.6"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1235A>G",
"hgvs_p": "p.Asp412Gly",
"transcript": "ENST00000877202.1",
"protein_id": "ENSP00000547261.1",
"transcript_support_level": null,
"aa_start": 412,
"aa_end": null,
"aa_length": 599,
"cds_start": 1235,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1324,
"cdna_end": null,
"cdna_length": 2632,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877202.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1235A>G",
"hgvs_p": "p.Asp412Gly",
"transcript": "ENST00000929484.1",
"protein_id": "ENSP00000599543.1",
"transcript_support_level": null,
"aa_start": 412,
"aa_end": null,
"aa_length": 592,
"cds_start": 1235,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 1291,
"cdna_end": null,
"cdna_length": 2351,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929484.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1181A>G",
"hgvs_p": "p.Asp394Gly",
"transcript": "ENST00000929486.1",
"protein_id": "ENSP00000599545.1",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 581,
"cds_start": 1181,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 1234,
"cdna_end": null,
"cdna_length": 1984,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929486.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1181A>G",
"hgvs_p": "p.Asp394Gly",
"transcript": "ENST00000942735.1",
"protein_id": "ENSP00000612794.1",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 574,
"cds_start": 1181,
"cds_end": null,
"cds_length": 1725,
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{
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{
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},
{
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],
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{
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],
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},
{
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},
{
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],
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000675234.1"
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],
"gene_symbol": "NGLY1",
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"dbsnp": "rs778513258",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.25216472148895264,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.048,
"revel_prediction": "Benign",
"alphamissense_score": 0.1005,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.871,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018297.4",
"gene_symbol": "NGLY1",
"hgnc_id": 17646,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1235A>G",
"hgvs_p": "p.Asp412Gly"
}
],
"clinvar_disease": "Congenital disorder of deglycosylation",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Congenital disorder of deglycosylation",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}