X-111680917-TG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000487141.5(ALG13):c.118-1214del variant causes a intron, NMD transcript 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, NMD_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALG13	ENST00000487141.5	c.118-1214del		intron_variant, NMD_transcript_variant		5

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

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 20, 2019

- -

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;