rs200121020

Variant names:

• chrX-111680917-TG-T
• rs200121020
• ENST00000487141.5:n.118-1214delG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000487141.5(ALG13):​n.118-1214delG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.075 (728 hom., 2189 hem., cov: 20)
• Consequence: ALG13 ENST00000487141.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.170
• Publications: 0 publications found

Genes affected

ALG13 (HGNC:30881): (ALG13 UDP-N-acetylglucosaminyltransferase subunit) The protein encoded by this gene is a subunit of a bipartite UDP-N-acetylglucosamine transferase. It heterodimerizes with asparagine-linked glycosylation 14 homolog to form a functional UDP-GlcNAc glycosyltransferase that catalyzes the second sugar addition of the highly conserved oligosaccharide precursor in endoplasmic reticulum N-linked glycosylation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]

ALG13 Gene-Disease associations (from GenCC):

• genetic developmental and epileptic encephalopathy

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• developmental and epileptic encephalopathy, 36

  Inheritance: XL Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
• non-syndromic X-linked intellectual disability

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant X-111680917-TG-T is Benign according to our data. Variant chrX-111680917-TG-T is described in ClinVar as [Benign]. Clinvar id is 1239678.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALG13	ENST00000487141.5	n.118-1214delG		intron_variant	Intron 1 of 6	5		ENSP00000478130.1
ALG13	ENST00000371979.7	c.-301delG		upstream_gene_variant		1		ENSP00000361047.3
ALG13	ENST00000623622.2	c.-301delG		upstream_gene_variant		5		ENSP00000485624.2

Frequencies

GnomAD3 genomes AF: 0.0748 AC: 8362 AN: 111766 Hom.: 727 Cov.: 20

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00329

Gnomad FIN AF: 0.000495

Gnomad MID AF: 0.0338

Gnomad NFE AF: 0.00450

Gnomad OTH AF: 0.0577

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0748 AC: 8364 AN: 111809 Hom.: 728 Cov.: 20 AF XY: 0.0642 AC XY: 2189 AN XY: 34109

African (AFR) AF: 0.248 AC: 7590 AN: 30627

American (AMR) AF: 0.0374 AC: 400 AN: 10692

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 32 AN: 2649

East Asian (EAS) AF: 0.00 AC: 0 AN: 3548

South Asian (SAS) AF: 0.00257 AC: 7 AN: 2728

European-Finnish (FIN) AF: 0.000495 AC: 3 AN: 6059

Middle Eastern (MID) AF: 0.0279 AC: 6 AN: 215

European-Non Finnish (NFE) AF: 0.00450 AC: 239 AN: 53081

Other (OTH) AF: 0.0570 AC: 87 AN: 1525

Alfa AF: 0.00266 Hom.: 11

Asia WGS AF: 0.0130 AC: 34 AN: 2521

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 20, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs200121020; hg19: chrX-110924145;