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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: 3-25720063-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=25720063&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 25720063,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_018297.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1740A>G",
"hgvs_p": "p.Thr580Thr",
"transcript": "NM_018297.4",
"protein_id": "NP_060767.2",
"transcript_support_level": null,
"aa_start": 580,
"aa_end": null,
"aa_length": 654,
"cds_start": 1740,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1793,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": "ENST00000280700.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018297.4"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1740A>G",
"hgvs_p": "p.Thr580Thr",
"transcript": "ENST00000280700.10",
"protein_id": "ENSP00000280700.5",
"transcript_support_level": 1,
"aa_start": 580,
"aa_end": null,
"aa_length": 654,
"cds_start": 1740,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1793,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": "NM_018297.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000280700.10"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1686A>G",
"hgvs_p": "p.Thr562Thr",
"transcript": "ENST00000428257.5",
"protein_id": "ENSP00000387430.1",
"transcript_support_level": 1,
"aa_start": 562,
"aa_end": null,
"aa_length": 636,
"cds_start": 1686,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 1794,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000428257.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1677A>G",
"hgvs_p": "p.Thr559Thr",
"transcript": "ENST00000308710.9",
"protein_id": "ENSP00000307980.5",
"transcript_support_level": 1,
"aa_start": 559,
"aa_end": null,
"aa_length": 633,
"cds_start": 1677,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 1677,
"cdna_end": null,
"cdna_length": 2086,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000308710.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1612-428A>G",
"hgvs_p": null,
"transcript": "ENST00000396649.7",
"protein_id": "ENSP00000379886.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 558,
"cds_start": null,
"cds_end": null,
"cds_length": 1677,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2024,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396649.7"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.1547A>G",
"hgvs_p": null,
"transcript": "ENST00000489271.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2288,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000489271.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1830A>G",
"hgvs_p": "p.Thr610Thr",
"transcript": "ENST00000877204.1",
"protein_id": "ENSP00000547263.1",
"transcript_support_level": null,
"aa_start": 610,
"aa_end": null,
"aa_length": 684,
"cds_start": 1830,
"cds_end": null,
"cds_length": 2055,
"cdna_start": 1883,
"cdna_end": null,
"cdna_length": 2293,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877204.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1824A>G",
"hgvs_p": "p.Thr608Thr",
"transcript": "ENST00000877207.1",
"protein_id": "ENSP00000547266.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 682,
"cds_start": 1824,
"cds_end": null,
"cds_length": 2049,
"cdna_start": 1835,
"cdna_end": null,
"cdna_length": 2249,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877207.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1797A>G",
"hgvs_p": "p.Thr599Thr",
"transcript": "ENST00000942732.1",
"protein_id": "ENSP00000612791.1",
"transcript_support_level": null,
"aa_start": 599,
"aa_end": null,
"aa_length": 673,
"cds_start": 1797,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 1898,
"cdna_end": null,
"cdna_length": 2313,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942732.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1791A>G",
"hgvs_p": "p.Thr597Thr",
"transcript": "ENST00000942731.1",
"protein_id": "ENSP00000612790.1",
"transcript_support_level": null,
"aa_start": 597,
"aa_end": null,
"aa_length": 671,
"cds_start": 1791,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 1842,
"cdna_end": null,
"cdna_length": 2580,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942731.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1743A>G",
"hgvs_p": "p.Thr581Thr",
"transcript": "ENST00000942734.1",
"protein_id": "ENSP00000612793.1",
"transcript_support_level": null,
"aa_start": 581,
"aa_end": null,
"aa_length": 655,
"cds_start": 1743,
"cds_end": null,
"cds_length": 1968,
"cdna_start": 1795,
"cdna_end": null,
"cdna_length": 2225,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942734.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1740A>G",
"hgvs_p": "p.Thr580Thr",
"transcript": "ENST00000942730.1",
"protein_id": "ENSP00000612789.1",
"transcript_support_level": null,
"aa_start": 580,
"aa_end": null,
"aa_length": 654,
"cds_start": 1740,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1793,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942730.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1737A>G",
"hgvs_p": "p.Thr579Thr",
"transcript": "ENST00000942736.1",
"protein_id": "ENSP00000612795.1",
"transcript_support_level": null,
"aa_start": 579,
"aa_end": null,
"aa_length": 653,
"cds_start": 1737,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 1761,
"cdna_end": null,
"cdna_length": 2163,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942736.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1716A>G",
"hgvs_p": "p.Thr572Thr",
"transcript": "ENST00000877206.1",
"protein_id": "ENSP00000547265.1",
"transcript_support_level": null,
"aa_start": 572,
"aa_end": null,
"aa_length": 646,
"cds_start": 1716,
"cds_end": null,
"cds_length": 1941,
"cdna_start": 1770,
"cdna_end": null,
"cdna_length": 2160,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877206.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1710A>G",
"hgvs_p": "p.Thr570Thr",
"transcript": "ENST00000676225.1",
"protein_id": "ENSP00000501622.1",
"transcript_support_level": null,
"aa_start": 570,
"aa_end": null,
"aa_length": 644,
"cds_start": 1710,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 1744,
"cdna_end": null,
"cdna_length": 2253,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676225.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1692A>G",
"hgvs_p": "p.Thr564Thr",
"transcript": "ENST00000942733.1",
"protein_id": "ENSP00000612792.1",
"transcript_support_level": null,
"aa_start": 564,
"aa_end": null,
"aa_length": 638,
"cds_start": 1692,
"cds_end": null,
"cds_length": 1917,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 2177,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942733.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1686A>G",
"hgvs_p": "p.Thr562Thr",
"transcript": "NM_001145293.2",
"protein_id": "NP_001138765.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 636,
"cds_start": 1686,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 1739,
"cdna_end": null,
"cdna_length": 2480,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145293.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1659A>G",
"hgvs_p": "p.Thr553Thr",
"transcript": "ENST00000877203.1",
"protein_id": "ENSP00000547262.1",
"transcript_support_level": null,
"aa_start": 553,
"aa_end": null,
"aa_length": 627,
"cds_start": 1659,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 1714,
"cdna_end": null,
"cdna_length": 2124,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877203.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1614A>G",
"hgvs_p": "p.Thr538Thr",
"transcript": "NM_001145294.2",
"protein_id": "NP_001138766.1",
"transcript_support_level": null,
"aa_start": 538,
"aa_end": null,
"aa_length": 612,
"cds_start": 1614,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1788,
"cdna_end": null,
"cdna_length": 2529,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145294.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.1614A>G",
"hgvs_p": "p.Thr538Thr",
"transcript": "ENST00000417874.6",
"protein_id": "ENSP00000389888.2",
"transcript_support_level": 2,
"aa_start": 538,
"aa_end": null,
"aa_length": 612,
"cds_start": 1614,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1788,
"cdna_end": null,
"cdna_length": 2062,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000417874.6"
},
{
"aa_ref": "T",
"aa_alt": "T",
"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.1575A>G",
"hgvs_p": "p.Thr525Thr",
"transcript": "ENST00000877202.1",
"protein_id": "ENSP00000547261.1",
"transcript_support_level": null,
"aa_start": 525,
"aa_end": null,
"aa_length": 599,
"cds_start": 1575,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1664,
"cdna_end": null,
"cdna_length": 2632,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877202.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"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.1554A>G",
"hgvs_p": "p.Thr518Thr",
"transcript": "ENST00000929484.1",
"protein_id": "ENSP00000599543.1",
"transcript_support_level": null,
"aa_start": 518,
"aa_end": null,
"aa_length": 592,
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"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000280699.13"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.*1831A>G",
"hgvs_p": null,
"transcript": "ENST00000463611.2",
"protein_id": "ENSP00000501918.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
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"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 2449,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000463611.2"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.*1113A>G",
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"transcript": "ENST00000675217.1",
"protein_id": "ENSP00000502195.1",
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"aa_start": null,
"aa_end": null,
"aa_length": null,
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"cds_end": null,
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"cdna_start": null,
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"cdna_length": 2532,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000675217.1"
},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
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"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.*1237A>G",
"hgvs_p": null,
"transcript": "ENST00000675234.1",
"protein_id": "ENSP00000502740.1",
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"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2166,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000675234.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.361+67A>G",
"hgvs_p": null,
"transcript": "ENST00000467224.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 722,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000467224.5"
}
],
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"dbsnp": "rs554503189",
"frequency_reference_population": 0.00010037585,
"hom_count_reference_population": 3,
"allele_count_reference_population": 162,
"gnomad_exomes_af": 0.00010673,
"gnomad_genomes_af": 0.000039397,
"gnomad_exomes_ac": 156,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"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": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.167,
"phylop100way_prediction": "Benign",
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_018297.4",
"gene_symbol": "NGLY1",
"hgnc_id": 17646,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1740A>G",
"hgvs_p": "p.Thr580Thr"
}
],
"clinvar_disease": "Congenital disorder of deglycosylation,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "Congenital disorder of deglycosylation|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}