← Back to variant description
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: 3-25729207-TTTGA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=25729207&ref=TTTGA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 25729207,
"ref": "TTTGA",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "ENST00000280700.10",
"consequences": [
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1533_1536delTCAA",
"hgvs_p": "p.Asn511fs",
"transcript": "NM_018297.4",
"protein_id": "NP_060767.2",
"transcript_support_level": null,
"aa_start": 511,
"aa_end": null,
"aa_length": 654,
"cds_start": 1533,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1589,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": "ENST00000280700.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1533_1536delTCAA",
"hgvs_p": "p.Asn511fs",
"transcript": "ENST00000280700.10",
"protein_id": "ENSP00000280700.5",
"transcript_support_level": 1,
"aa_start": 511,
"aa_end": null,
"aa_length": 654,
"cds_start": 1533,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1589,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": "NM_018297.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1479_1482delTCAA",
"hgvs_p": "p.Asn493fs",
"transcript": "ENST00000428257.5",
"protein_id": "ENSP00000387430.1",
"transcript_support_level": 1,
"aa_start": 493,
"aa_end": null,
"aa_length": 636,
"cds_start": 1479,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 1590,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1470_1473delTCAA",
"hgvs_p": "p.Asn490fs",
"transcript": "ENST00000308710.9",
"protein_id": "ENSP00000307980.5",
"transcript_support_level": 1,
"aa_start": 490,
"aa_end": null,
"aa_length": 633,
"cds_start": 1470,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 1473,
"cdna_end": null,
"cdna_length": 2086,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1533_1536delTCAA",
"hgvs_p": "p.Asn511fs",
"transcript": "ENST00000396649.7",
"protein_id": "ENSP00000379886.3",
"transcript_support_level": 1,
"aa_start": 511,
"aa_end": null,
"aa_length": 558,
"cds_start": 1533,
"cds_end": null,
"cds_length": 1677,
"cdna_start": 1584,
"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.1340_1343delTCAA",
"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": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1503_1506delTCAA",
"hgvs_p": "p.Asn501fs",
"transcript": "ENST00000676225.1",
"protein_id": "ENSP00000501622.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 644,
"cds_start": 1503,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 1540,
"cdna_end": null,
"cdna_length": 2253,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1479_1482delTCAA",
"hgvs_p": "p.Asn493fs",
"transcript": "NM_001145293.2",
"protein_id": "NP_001138765.1",
"transcript_support_level": null,
"aa_start": 493,
"aa_end": null,
"aa_length": 636,
"cds_start": 1479,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 1535,
"cdna_end": null,
"cdna_length": 2480,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1407_1410delTCAA",
"hgvs_p": "p.Asn469fs",
"transcript": "NM_001145294.2",
"protein_id": "NP_001138766.1",
"transcript_support_level": null,
"aa_start": 469,
"aa_end": null,
"aa_length": 612,
"cds_start": 1407,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1584,
"cdna_end": null,
"cdna_length": 2529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1407_1410delTCAA",
"hgvs_p": "p.Asn469fs",
"transcript": "ENST00000417874.6",
"protein_id": "ENSP00000389888.2",
"transcript_support_level": 2,
"aa_start": 469,
"aa_end": null,
"aa_length": 612,
"cds_start": 1407,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1584,
"cdna_end": null,
"cdna_length": 2062,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1533_1536delTCAA",
"hgvs_p": "p.Asn511fs",
"transcript": "NM_001145295.2",
"protein_id": "NP_001138767.1",
"transcript_support_level": null,
"aa_start": 511,
"aa_end": null,
"aa_length": 558,
"cds_start": 1533,
"cds_end": null,
"cds_length": 1677,
"cdna_start": 1589,
"cdna_end": null,
"cdna_length": 2356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.846_849delTCAA",
"hgvs_p": "p.Asn282fs",
"transcript": "ENST00000675680.1",
"protein_id": "ENSP00000502709.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 425,
"cds_start": 846,
"cds_end": null,
"cds_length": 1278,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 1464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1368_1371delTCAA",
"hgvs_p": "p.Asn456fs",
"transcript": "XM_005265316.1",
"protein_id": "XP_005265373.1",
"transcript_support_level": null,
"aa_start": 456,
"aa_end": null,
"aa_length": 599,
"cds_start": 1368,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1424,
"cdna_end": null,
"cdna_length": 2369,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1533_1536delTCAA",
"hgvs_p": "p.Asn511fs",
"transcript": "XM_017006839.3",
"protein_id": "XP_016862328.1",
"transcript_support_level": null,
"aa_start": 511,
"aa_end": null,
"aa_length": 591,
"cds_start": 1533,
"cds_end": null,
"cds_length": 1776,
"cdna_start": 1589,
"cdna_end": null,
"cdna_length": 1887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1314_1317delTCAA",
"hgvs_p": "p.Asn438fs",
"transcript": "XM_047448556.1",
"protein_id": "XP_047304512.1",
"transcript_support_level": null,
"aa_start": 438,
"aa_end": null,
"aa_length": 581,
"cds_start": 1314,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 1370,
"cdna_end": null,
"cdna_length": 2315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1302_1305delTCAA",
"hgvs_p": "p.Asn434fs",
"transcript": "XM_011533944.1",
"protein_id": "XP_011532246.1",
"transcript_support_level": null,
"aa_start": 434,
"aa_end": null,
"aa_length": 577,
"cds_start": 1302,
"cds_end": null,
"cds_length": 1734,
"cdna_start": 1540,
"cdna_end": null,
"cdna_length": 2485,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1479_1482delTCAA",
"hgvs_p": "p.Asn493fs",
"transcript": "XM_047448557.1",
"protein_id": "XP_047304513.1",
"transcript_support_level": null,
"aa_start": 493,
"aa_end": null,
"aa_length": 540,
"cds_start": 1479,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1535,
"cdna_end": null,
"cdna_length": 2302,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1368_1371delTCAA",
"hgvs_p": "p.Asn456fs",
"transcript": "XM_005265317.1",
"protein_id": "XP_005265374.1",
"transcript_support_level": null,
"aa_start": 456,
"aa_end": null,
"aa_length": 503,
"cds_start": 1368,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 1424,
"cdna_end": null,
"cdna_length": 2191,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.1314_1317delTCAA",
"hgvs_p": "p.Asn438fs",
"transcript": "XM_047448558.1",
"protein_id": "XP_047304514.1",
"transcript_support_level": null,
"aa_start": 438,
"aa_end": null,
"aa_length": 485,
"cds_start": 1314,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 1370,
"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.*563_*566delTCAA",
"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.*1624_*1627delTCAA",
"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.221_224delTCAA",
"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.2436_2439delTCAA",
"hgvs_p": null,
"transcript": "ENST00000493324.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 3058,
"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.2583_2586delTCAA",
"hgvs_p": null,
"transcript": "ENST00000496726.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 3196,
"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": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.1656_1659delTCAA",
"hgvs_p": null,
"transcript": "ENST00000674841.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2235,
"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": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.551_554delTCAA",
"hgvs_p": null,
"transcript": "ENST00000675178.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1413,
"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": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.*906_*909delTCAA",
"hgvs_p": null,
"transcript": "ENST00000675217.1",
"protein_id": "ENSP00000502195.1",
"transcript_support_level": null,
"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": 2532,
"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": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.*1030_*1033delTCAA",
"hgvs_p": null,
"transcript": "ENST00000675234.1",
"protein_id": "ENSP00000502740.1",
"transcript_support_level": null,
"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": 2166,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_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.*563_*566delTCAA",
"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": [
"3_prime_UTR_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.*1624_*1627delTCAA",
"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": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.*906_*909delTCAA",
"hgvs_p": null,
"transcript": "ENST00000675217.1",
"protein_id": "ENSP00000502195.1",
"transcript_support_level": null,
"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": 2532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.*1030_*1033delTCAA",
"hgvs_p": null,
"transcript": "ENST00000675234.1",
"protein_id": "ENSP00000502740.1",
"transcript_support_level": null,
"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": 2166,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"dbsnp": "rs765211108",
"frequency_reference_population": 0.000017845761,
"hom_count_reference_population": 0,
"allele_count_reference_population": 28,
"gnomad_exomes_af": 0.0000190561,
"gnomad_genomes_af": 0.00000657341,
"gnomad_exomes_ac": 27,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 3.803,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000280700.10",
"gene_symbol": "NGLY1",
"hgnc_id": 17646,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1533_1536delTCAA",
"hgvs_p": "p.Asn511fs"
}
],
"clinvar_disease": "Congenital disorder of deglycosylation,Congenital disorder of deglycosylation 1,Intellectual disability,Neuromotor delay,Peripheral neuropathy,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5",
"phenotype_combined": "Intellectual disability;Neuromotor delay;Peripheral neuropathy|Congenital disorder of deglycosylation|not provided|Congenital disorder of deglycosylation 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}