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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: 1-119737114-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=119737114&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 119737114,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000641023.2",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.793G>A",
"hgvs_p": "p.Glu265Lys",
"transcript": "NM_006623.4",
"protein_id": "NP_006614.2",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 533,
"cds_start": 793,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 1866,
"mane_select": "ENST00000641023.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.793G>A",
"hgvs_p": "p.Glu265Lys",
"transcript": "ENST00000641023.2",
"protein_id": "ENSP00000493175.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 533,
"cds_start": 793,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 1866,
"mane_select": "NM_006623.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.793G>A",
"hgvs_p": "p.Glu265Lys",
"transcript": "ENST00000369409.9",
"protein_id": "ENSP00000358417.5",
"transcript_support_level": 1,
"aa_start": 265,
"aa_end": null,
"aa_length": 532,
"cds_start": 793,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 1882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.793G>A",
"hgvs_p": "p.Glu265Lys",
"transcript": "ENST00000641597.1",
"protein_id": "ENSP00000493382.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 533,
"cds_start": 793,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 1626,
"cdna_end": null,
"cdna_length": 2585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.793G>A",
"hgvs_p": "p.Glu265Lys",
"transcript": "ENST00000641947.1",
"protein_id": "ENSP00000492994.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 526,
"cds_start": 793,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 932,
"cdna_end": null,
"cdna_length": 1774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.793G>A",
"hgvs_p": "p.Glu265Lys",
"transcript": "ENST00000641115.1",
"protein_id": "ENSP00000493264.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 445,
"cds_start": 793,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 918,
"cdna_end": null,
"cdna_length": 1638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.793G>A",
"hgvs_p": "p.Glu265Lys",
"transcript": "ENST00000641074.1",
"protein_id": "ENSP00000493446.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 429,
"cds_start": 793,
"cds_end": null,
"cds_length": 1290,
"cdna_start": 930,
"cdna_end": null,
"cdna_length": 1780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.547G>A",
"hgvs_p": "p.Glu183Lys",
"transcript": "ENST00000641811.1",
"protein_id": "ENSP00000493296.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 275,
"cds_start": 547,
"cds_end": null,
"cds_length": 828,
"cdna_start": 549,
"cdna_end": null,
"cdna_length": 1031,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.1015G>A",
"hgvs_p": "p.Glu339Lys",
"transcript": "XM_011541226.3",
"protein_id": "XP_011539528.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 607,
"cds_start": 1015,
"cds_end": null,
"cds_length": 1824,
"cdna_start": 1104,
"cdna_end": null,
"cdna_length": 2088,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.937G>A",
"hgvs_p": "p.Glu313Lys",
"transcript": "XM_011541227.3",
"protein_id": "XP_011539529.1",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 581,
"cds_start": 937,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 1005,
"cdna_end": null,
"cdna_length": 1989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.904G>A",
"hgvs_p": "p.Glu302Lys",
"transcript": "XM_011541228.3",
"protein_id": "XP_011539530.1",
"transcript_support_level": null,
"aa_start": 302,
"aa_end": null,
"aa_length": 570,
"cds_start": 904,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 919,
"cdna_end": null,
"cdna_length": 1903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.730G>A",
"hgvs_p": "p.Glu244Lys",
"transcript": "XM_047417680.1",
"protein_id": "XP_047273636.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 512,
"cds_start": 730,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 1426,
"cdna_end": null,
"cdna_length": 2410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.508G>A",
"hgvs_p": "p.Glu170Lys",
"transcript": "XM_047417682.1",
"protein_id": "XP_047273638.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 438,
"cds_start": 508,
"cds_end": null,
"cds_length": 1317,
"cdna_start": 1192,
"cdna_end": null,
"cdna_length": 2176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.499G>A",
"hgvs_p": "p.Glu167Lys",
"transcript": "XM_047417683.1",
"protein_id": "XP_047273639.1",
"transcript_support_level": null,
"aa_start": 167,
"aa_end": null,
"aa_length": 435,
"cds_start": 499,
"cds_end": null,
"cds_length": 1308,
"cdna_start": 628,
"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": [
"splice_region_variant",
"non_coding_transcript_exon_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": "n.2198G>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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.613G>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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.*446G>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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.778G>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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.*629G>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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.*537G>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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.*619G>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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.733G>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,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
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},
{
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"transcript": "ENST00000641213.1",
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},
{
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"gene_symbol": "PHGDH",
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"transcript": "ENST00000641375.1",
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},
{
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"gene_symbol": "PHGDH",
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"transcript": "ENST00000641756.1",
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},
{
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"gene_symbol": "PHGDH",
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"transcript": "ENST00000641891.1",
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},
{
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"consequences": [
"upstream_gene_variant"
],
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"gene_symbol": "PHGDH",
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"hgvs_c": "n.-105G>A",
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"transcript": "ENST00000641939.1",
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}
],
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"dbsnp": "rs587777774",
"frequency_reference_population": 6.841452e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84145e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9767410755157471,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9340000152587891,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.964,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9839,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.37,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.83,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.4,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.999383236340088,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3,PP5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PM2",
"PP3",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000641023.2",
"gene_symbol": "PHGDH",
"hgnc_id": 8923,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.793G>A",
"hgvs_p": "p.Glu265Lys"
}
],
"clinvar_disease": "Neu-Laxova syndrome 1",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Neu-Laxova syndrome 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}