← 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: 3-25783269-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=25783269&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 25783269,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_018297.4",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "NM_018297.4",
"protein_id": "NP_060767.2",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 654,
"cds_start": 122,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": "ENST00000280700.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018297.4"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000280700.10",
"protein_id": "ENSP00000280700.5",
"transcript_support_level": 1,
"aa_start": 41,
"aa_end": null,
"aa_length": 654,
"cds_start": 122,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": "NM_018297.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000280700.10"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000428257.5",
"protein_id": "ENSP00000387430.1",
"transcript_support_level": 1,
"aa_start": 41,
"aa_end": null,
"aa_length": 636,
"cds_start": 122,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 230,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000428257.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.113A>G",
"hgvs_p": "p.Asn38Ser",
"transcript": "ENST00000308710.9",
"protein_id": "ENSP00000307980.5",
"transcript_support_level": 1,
"aa_start": 38,
"aa_end": null,
"aa_length": 633,
"cds_start": 113,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 113,
"cdna_end": null,
"cdna_length": 2086,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000308710.9"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000396649.7",
"protein_id": "ENSP00000379886.3",
"transcript_support_level": 1,
"aa_start": 41,
"aa_end": null,
"aa_length": 558,
"cds_start": 122,
"cds_end": null,
"cds_length": 1677,
"cdna_start": 170,
"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": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSM",
"gene_hgnc_id": 26063,
"hgvs_c": "c.-64T>C",
"hgvs_p": null,
"transcript": "ENST00000942860.1",
"protein_id": "ENSP00000612919.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 459,
"cds_start": null,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1680,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942860.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSM",
"gene_hgnc_id": 26063,
"hgvs_c": "c.-43T>C",
"hgvs_p": null,
"transcript": "ENST00000452098.1",
"protein_id": "ENSP00000392334.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 219,
"cds_start": null,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 899,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452098.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000877204.1",
"protein_id": "ENSP00000547263.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 684,
"cds_start": 122,
"cds_end": null,
"cds_length": 2055,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2293,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877204.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000877207.1",
"protein_id": "ENSP00000547266.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 682,
"cds_start": 122,
"cds_end": null,
"cds_length": 2049,
"cdna_start": 133,
"cdna_end": null,
"cdna_length": 2249,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877207.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000942732.1",
"protein_id": "ENSP00000612791.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 673,
"cds_start": 122,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 223,
"cdna_end": null,
"cdna_length": 2313,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942732.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000942731.1",
"protein_id": "ENSP00000612790.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 671,
"cds_start": 122,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 173,
"cdna_end": null,
"cdna_length": 2580,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942731.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000942734.1",
"protein_id": "ENSP00000612793.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 655,
"cds_start": 122,
"cds_end": null,
"cds_length": 1968,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 2225,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942734.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000942730.1",
"protein_id": "ENSP00000612789.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 654,
"cds_start": 122,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942730.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000942736.1",
"protein_id": "ENSP00000612795.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 653,
"cds_start": 122,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 146,
"cdna_end": null,
"cdna_length": 2163,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942736.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000877206.1",
"protein_id": "ENSP00000547265.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 646,
"cds_start": 122,
"cds_end": null,
"cds_length": 1941,
"cdna_start": 176,
"cdna_end": null,
"cdna_length": 2160,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877206.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000676225.1",
"protein_id": "ENSP00000501622.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 644,
"cds_start": 122,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 156,
"cdna_end": null,
"cdna_length": 2253,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676225.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000942733.1",
"protein_id": "ENSP00000612792.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 638,
"cds_start": 122,
"cds_end": null,
"cds_length": 1917,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2177,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942733.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "NM_001145293.2",
"protein_id": "NP_001138765.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 636,
"cds_start": 122,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2480,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145293.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000877203.1",
"protein_id": "ENSP00000547262.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 627,
"cds_start": 122,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 177,
"cdna_end": null,
"cdna_length": 2124,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877203.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000877202.1",
"protein_id": "ENSP00000547261.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 599,
"cds_start": 122,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 211,
"cdna_end": null,
"cdna_length": 2632,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877202.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000929484.1",
"protein_id": "ENSP00000599543.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 592,
"cds_start": 122,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 178,
"cdna_end": null,
"cdna_length": 2351,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929484.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000929486.1",
"protein_id": "ENSP00000599545.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 581,
"cds_start": 122,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 1984,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929486.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000942735.1",
"protein_id": "ENSP00000612794.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 574,
"cds_start": 122,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 1955,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942735.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "NM_001145295.2",
"protein_id": "NP_001138767.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 558,
"cds_start": 122,
"cds_end": null,
"cds_length": 1677,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2356,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145295.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000942729.1",
"protein_id": "ENSP00000612788.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 539,
"cds_start": 122,
"cds_end": null,
"cds_length": 1620,
"cdna_start": 177,
"cdna_end": null,
"cdna_length": 2190,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942729.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000929485.1",
"protein_id": "ENSP00000599544.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 521,
"cds_start": 122,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 172,
"cdna_end": null,
"cdna_length": 1807,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929485.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000877205.1",
"protein_id": "ENSP00000547264.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 489,
"cds_start": 122,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 1702,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877205.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "ENST00000929487.1",
"protein_id": "ENSP00000599546.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 434,
"cds_start": 122,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 1515,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929487.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "XM_005265316.1",
"protein_id": "XP_005265373.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 599,
"cds_start": 122,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2369,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005265316.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "XM_017006839.3",
"protein_id": "XP_016862328.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 591,
"cds_start": 122,
"cds_end": null,
"cds_length": 1776,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 1887,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006839.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "XM_047448556.1",
"protein_id": "XP_047304512.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 581,
"cds_start": 122,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2315,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448556.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "XM_047448557.1",
"protein_id": "XP_047304513.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 540,
"cds_start": 122,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2302,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448557.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "XM_005265317.1",
"protein_id": "XP_005265374.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 503,
"cds_start": 122,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2191,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005265317.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "XM_047448558.1",
"protein_id": "XP_047304514.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 485,
"cds_start": 122,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2137,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448558.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "XM_047448560.1",
"protein_id": "XP_047304516.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 397,
"cds_start": 122,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 1405,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448560.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser",
"transcript": "XM_047448561.1",
"protein_id": "XP_047304517.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 336,
"cds_start": 122,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 1167,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448561.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSM",
"gene_hgnc_id": 26063,
"hgvs_c": "c.-64T>C",
"hgvs_p": null,
"transcript": "ENST00000942860.1",
"protein_id": "ENSP00000612919.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 459,
"cds_start": null,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1680,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942860.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSM",
"gene_hgnc_id": 26063,
"hgvs_c": "c.-43T>C",
"hgvs_p": null,
"transcript": "ENST00000452098.1",
"protein_id": "ENSP00000392334.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 219,
"cds_start": null,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 899,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452098.1"
},
{
"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": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.6-4581A>G",
"hgvs_p": null,
"transcript": "NM_001145294.2",
"protein_id": "NP_001138766.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 612,
"cds_start": null,
"cds_end": null,
"cds_length": 1839,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2529,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145294.2"
},
{
"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": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "c.6-4581A>G",
"hgvs_p": null,
"transcript": "ENST00000417874.6",
"protein_id": "ENSP00000389888.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 612,
"cds_start": null,
"cds_end": null,
"cds_length": 1839,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2062,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000417874.6"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.95A>G",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1897,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000280699.13"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSM",
"gene_hgnc_id": 26063,
"hgvs_c": "n.353T>C",
"hgvs_p": null,
"transcript": "ENST00000460195.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 410,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000460195.1"
},
{
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.122A>G",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2449,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000463611.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSM",
"gene_hgnc_id": 26063,
"hgvs_c": "n.231T>C",
"hgvs_p": null,
"transcript": "ENST00000464688.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 462,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000464688.1"
},
{
"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.214A>G",
"hgvs_p": null,
"transcript": "ENST00000474611.1",
"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": 478,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000474611.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.146A>G",
"hgvs_p": null,
"transcript": "ENST00000478991.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 582,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000478991.1"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.146A>G",
"hgvs_p": null,
"transcript": "ENST00000493324.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 3058,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000493324.5"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.122A>G",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2532,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000675217.1"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.122A>G",
"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": 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,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"hgvs_c": "n.114+774A>G",
"hgvs_p": null,
"transcript": "ENST00000461491.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 552,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000461491.5"
}
],
"gene_symbol": "NGLY1",
"gene_hgnc_id": 17646,
"dbsnp": null,
"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": 0.97332763671875,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.453,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9108,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.64,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_018297.4",
"gene_symbol": "NGLY1",
"hgnc_id": 17646,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Asn41Ser"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000452098.1",
"gene_symbol": "OXSM",
"hgnc_id": 26063,
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-43T>C",
"hgvs_p": null
}
],
"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
}