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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: 1-119735394-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=119735394&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 119735394,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000641023.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.743C>A",
"hgvs_p": "p.Ala248Asp",
"transcript": "NM_006623.4",
"protein_id": "NP_006614.2",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 533,
"cds_start": 743,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 1866,
"mane_select": "ENST00000641023.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.743C>A",
"hgvs_p": "p.Ala248Asp",
"transcript": "ENST00000641023.2",
"protein_id": "ENSP00000493175.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 533,
"cds_start": 743,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 1866,
"mane_select": "NM_006623.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.743C>A",
"hgvs_p": "p.Ala248Asp",
"transcript": "ENST00000369409.9",
"protein_id": "ENSP00000358417.5",
"transcript_support_level": 1,
"aa_start": 248,
"aa_end": null,
"aa_length": 532,
"cds_start": 743,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 1882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.743C>A",
"hgvs_p": "p.Ala248Asp",
"transcript": "ENST00000641597.1",
"protein_id": "ENSP00000493382.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 533,
"cds_start": 743,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 1576,
"cdna_end": null,
"cdna_length": 2585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.743C>A",
"hgvs_p": "p.Ala248Asp",
"transcript": "ENST00000641947.1",
"protein_id": "ENSP00000492994.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 526,
"cds_start": 743,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 1774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.743C>A",
"hgvs_p": "p.Ala248Asp",
"transcript": "ENST00000641115.1",
"protein_id": "ENSP00000493264.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 445,
"cds_start": 743,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 868,
"cdna_end": null,
"cdna_length": 1638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.743C>A",
"hgvs_p": "p.Ala248Asp",
"transcript": "ENST00000641074.1",
"protein_id": "ENSP00000493446.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 429,
"cds_start": 743,
"cds_end": null,
"cds_length": 1290,
"cdna_start": 880,
"cdna_end": null,
"cdna_length": 1780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.497C>A",
"hgvs_p": "p.Ala166Asp",
"transcript": "ENST00000641811.1",
"protein_id": "ENSP00000493296.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 275,
"cds_start": 497,
"cds_end": null,
"cds_length": 828,
"cdna_start": 499,
"cdna_end": null,
"cdna_length": 1031,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.677C>A",
"hgvs_p": "p.Ala226Asp",
"transcript": "ENST00000641272.1",
"protein_id": "ENSP00000493432.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 238,
"cds_start": 677,
"cds_end": null,
"cds_length": 718,
"cdna_start": 717,
"cdna_end": null,
"cdna_length": 758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.965C>A",
"hgvs_p": "p.Ala322Asp",
"transcript": "XM_011541226.3",
"protein_id": "XP_011539528.1",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 607,
"cds_start": 965,
"cds_end": null,
"cds_length": 1824,
"cdna_start": 1054,
"cdna_end": null,
"cdna_length": 2088,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.887C>A",
"hgvs_p": "p.Ala296Asp",
"transcript": "XM_011541227.3",
"protein_id": "XP_011539529.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 581,
"cds_start": 887,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 955,
"cdna_end": null,
"cdna_length": 1989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.854C>A",
"hgvs_p": "p.Ala285Asp",
"transcript": "XM_011541228.3",
"protein_id": "XP_011539530.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 570,
"cds_start": 854,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 869,
"cdna_end": null,
"cdna_length": 1903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.680C>A",
"hgvs_p": "p.Ala227Asp",
"transcript": "XM_047417680.1",
"protein_id": "XP_047273636.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 512,
"cds_start": 680,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 1376,
"cdna_end": null,
"cdna_length": 2410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.458C>A",
"hgvs_p": "p.Ala153Asp",
"transcript": "XM_047417682.1",
"protein_id": "XP_047273638.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 438,
"cds_start": 458,
"cds_end": null,
"cds_length": 1317,
"cdna_start": 1142,
"cdna_end": null,
"cdna_length": 2176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.449C>A",
"hgvs_p": "p.Ala150Asp",
"transcript": "XM_047417683.1",
"protein_id": "XP_047273639.1",
"transcript_support_level": null,
"aa_start": 150,
"aa_end": null,
"aa_length": 435,
"cds_start": 449,
"cds_end": null,
"cds_length": 1308,
"cdna_start": 578,
"cdna_end": null,
"cdna_length": 1612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.2148C>A",
"hgvs_p": null,
"transcript": "ENST00000369407.3",
"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": 3180,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.563C>A",
"hgvs_p": null,
"transcript": "ENST00000469443.2",
"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": 653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.*396C>A",
"hgvs_p": null,
"transcript": "ENST00000641213.1",
"protein_id": "ENSP00000493079.1",
"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": 2053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.728C>A",
"hgvs_p": null,
"transcript": "ENST00000641314.1",
"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": 1558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.*579C>A",
"hgvs_p": null,
"transcript": "ENST00000641375.1",
"protein_id": "ENSP00000493089.1",
"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": 2196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.*487C>A",
"hgvs_p": null,
"transcript": "ENST00000641756.1",
"protein_id": "ENSP00000493147.1",
"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": 2132,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.*569C>A",
"hgvs_p": null,
"transcript": "ENST00000641891.1",
"protein_id": "ENSP00000493288.1",
"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": 2175,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.683C>A",
"hgvs_p": null,
"transcript": "ENST00000641927.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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},
{
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"canonical": false,
"protein_coding": false,
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},
{
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},
{
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},
{
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"gene_symbol": "PHGDH",
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"transcript": "ENST00000641756.1",
"protein_id": "ENSP00000493147.1",
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},
{
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},
{
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"downstream_gene_variant"
],
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"gene_symbol": "PHGDH",
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},
{
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],
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"gene_symbol": "PHGDH",
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"hgvs_c": "n.*219C>A",
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"transcript": "ENST00000641371.1",
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"cdna_length": 725,
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"feature": null
}
],
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"dbsnp": "rs201782441",
"frequency_reference_population": 0.0000027364497,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273645,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9505964517593384,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.904,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9283,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.675,
"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": "ENST00000641023.2",
"gene_symbol": "PHGDH",
"hgnc_id": 8923,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.743C>A",
"hgvs_p": "p.Ala248Asp"
}
],
"clinvar_disease": "Inborn genetic diseases,Neu-Laxova syndrome 1,PHGDH deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "PHGDH deficiency|Inborn genetic diseases|Neu-Laxova syndrome 1",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}