← 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: 1-119712044-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=119712044&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 119712044,
"ref": "A",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_006623.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "NM_006623.4",
"protein_id": "NP_006614.2",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 533,
"cds_start": 22,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000641023.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006623.4"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000641023.2",
"protein_id": "ENSP00000493175.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 533,
"cds_start": 22,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006623.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000641023.2"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000369409.9",
"protein_id": "ENSP00000358417.5",
"transcript_support_level": 1,
"aa_start": 8,
"aa_end": null,
"aa_length": 532,
"cds_start": 22,
"cds_end": null,
"cds_length": 1599,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369409.9"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000641597.1",
"protein_id": "ENSP00000493382.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 533,
"cds_start": 22,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000641597.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000641947.1",
"protein_id": "ENSP00000492994.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 526,
"cds_start": 22,
"cds_end": null,
"cds_length": 1581,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000641947.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000858460.1",
"protein_id": "ENSP00000528519.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 521,
"cds_start": 22,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858460.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000641115.1",
"protein_id": "ENSP00000493264.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 445,
"cds_start": 22,
"cds_end": null,
"cds_length": 1338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000641115.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000936419.1",
"protein_id": "ENSP00000606478.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 442,
"cds_start": 22,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936419.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000641074.1",
"protein_id": "ENSP00000493446.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 429,
"cds_start": 22,
"cds_end": null,
"cds_length": 1290,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000641074.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000936417.1",
"protein_id": "ENSP00000606476.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 409,
"cds_start": 22,
"cds_end": null,
"cds_length": 1230,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936417.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000641272.1",
"protein_id": "ENSP00000493432.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 238,
"cds_start": 22,
"cds_end": null,
"cds_length": 718,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000641272.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000936416.1",
"protein_id": "ENSP00000606475.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 176,
"cds_start": 22,
"cds_end": null,
"cds_length": 531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936416.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"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": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "ENST00000641720.1",
"protein_id": "ENSP00000492948.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 71,
"cds_start": 22,
"cds_end": null,
"cds_length": 216,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000641720.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*",
"transcript": "XM_011541226.3",
"protein_id": "XP_011539528.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 607,
"cds_start": 22,
"cds_end": null,
"cds_length": 1824,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541226.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "c.-147-9126A>T",
"hgvs_p": null,
"transcript": "ENST00000493622.5",
"protein_id": "ENSP00000493433.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 88,
"cds_start": null,
"cds_end": null,
"cds_length": 268,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000493622.5"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.105A>T",
"hgvs_p": null,
"transcript": "ENST00000462324.2",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000462324.2"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.158A>T",
"hgvs_p": null,
"transcript": "ENST00000496756.2",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000496756.2"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.22A>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000641213.1"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.22A>T",
"hgvs_p": null,
"transcript": "ENST00000641247.1",
"protein_id": "ENSP00000492955.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000641247.1"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.22A>T",
"hgvs_p": null,
"transcript": "ENST00000641371.1",
"protein_id": "ENSP00000493305.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000641371.1"
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.22A>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000641375.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.22A>T",
"hgvs_p": null,
"transcript": "ENST00000641491.1",
"protein_id": "ENSP00000493187.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000641491.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.22A>T",
"hgvs_p": null,
"transcript": "ENST00000641513.1",
"protein_id": "ENSP00000493398.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000641513.1"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.22A>T",
"hgvs_p": null,
"transcript": "ENST00000641570.1",
"protein_id": "ENSP00000493213.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000641570.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.110A>T",
"hgvs_p": null,
"transcript": "ENST00000641573.1",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000641573.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.22A>T",
"hgvs_p": null,
"transcript": "ENST00000641587.1",
"protein_id": "ENSP00000493453.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000641587.1"
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.22A>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000641891.1"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.144A>T",
"hgvs_p": null,
"transcript": "ENST00000642021.1",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000642021.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.22A>T",
"hgvs_p": null,
"transcript": "ENST00000642041.1",
"protein_id": "ENSP00000493415.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000642041.1"
},
{
"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": "ENSG00000296692",
"gene_hgnc_id": null,
"hgvs_c": "n.190T>A",
"hgvs_p": null,
"transcript": "ENST00000741201.1",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000741201.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"hgvs_c": "n.111A>T",
"hgvs_p": null,
"transcript": "XR_007058634.1",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007058634.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC105378937",
"gene_hgnc_id": null,
"hgvs_c": "n.-198T>A",
"hgvs_p": null,
"transcript": "XR_947757.4",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_947757.4"
}
],
"gene_symbol": "PHGDH",
"gene_hgnc_id": 8923,
"dbsnp": "rs1650717188",
"frequency_reference_population": 0.000013140777,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000131408,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.550000011920929,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.6899999976158142,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.723,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.69,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 13,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP3,PP5_Moderate",
"acmg_by_gene": [
{
"score": 13,
"benign_score": 0,
"pathogenic_score": 13,
"criteria": [
"PVS1",
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_006623.4",
"gene_symbol": "PHGDH",
"hgnc_id": 8923,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.22A>T",
"hgvs_p": "p.Lys8*"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000741201.1",
"gene_symbol": "ENSG00000296692",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.190T>A",
"hgvs_p": null
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "XR_947757.4",
"gene_symbol": "LOC105378937",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-198T>A",
"hgvs_p": null
}
],
"clinvar_disease": "PHGDH deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "PHGDH deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}