rs200121020

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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 AF XY: 0.0642 AC XY: 2186 AN XY: 34056

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

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.0374

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00257

Gnomad4 FIN AF: 0.000495

Gnomad4 NFE AF: 0.00450

Gnomad4 OTH AF: 0.0570

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200121020; hg19: chrX-110924145;