Variant chrX-111680917-TG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.170

Variant links:

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 links:

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ACMG classification

Classification made for transcript

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 linkuse as main transcript	c.118-1214del		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0748

AC:

8362

AN:

111766

Hom.:

727

Cov.:

AF XY:

0.0642

AC XY:

2186

AN XY:

34056

show subpopulations

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.:

AF XY:

0.0642

AC XY:

2189

AN XY:

34109

show subpopulations

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.:

Asia WGS

AF:

0.0130

AC:

AN:

2521

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 20, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over