Variant X-111744768-A-ACCT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_001099922.3(ALG13):c.2833_2835dupCCT(p.Pro945dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0207 in 575,972 control chromosomes in the GnomAD database, including 34 homozygotes. There are 1,089 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.037 ( 19 hom., 71 hem., cov: 18)

Exomes 𝑓: 0.020 ( 15 hom. 1018 hem. )

Consequence

ALG13
NM_001099922.3 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.159

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:

ALG13 (HGNC:):

ALG13 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant X-111744768-A-ACCT is Benign according to our data. Variant chrX-111744768-A-ACCT is described in ClinVar as [Benign]. Clinvar id is 1168196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0369 (1365/37008) while in subpopulation NFE AF= 0.0508 (1007/19831). AF 95% confidence interval is 0.0482. There are 19 homozygotes in gnomad4. There are 71 alleles in male gnomad4 subpopulation. Median coverage is 18. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 19 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALG13	NM_001099922.3 linkuse as main transcript	c.2833_2835dupCCT	p.Pro945dup	conservative_inframe_insertion	24/27	ENST00000394780.8	NP_001093392.1	Q9NP73-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALG13	ENST00000394780.8 linkuse as main transcript	c.2833_2835dupCCT	p.Pro945dup	conservative_inframe_insertion	24/27	2	NM_001099922.3	ENSP00000378260.3		Q9NP73-1

Frequencies

GnomAD3 genomes

AF:

0.0369

AC:

1365

AN:

37012

Hom.:

Cov.:

AF XY:

0.00997

AC XY:

AN XY:

7122

show subpopulations

Gnomad AFR

AF:

0.0116

Gnomad AMI

AF:

0.0221

Gnomad AMR

AF:

0.0328

Gnomad ASJ

AF:

0.0180

Gnomad EAS

AF:

0.0141

Gnomad SAS

AF:

0.00926

Gnomad FIN

AF:

0.0790

Gnomad MID

AF:

0.0110

Gnomad NFE

AF:

0.0508

Gnomad OTH

AF:

0.0451

GnomAD3 exomes

AF:

0.0265

AC:

880

AN:

33243

Hom.:

AF XY:

0.00635

AC XY:

AN XY:

5669

show subpopulations

Gnomad AFR exome

AF:

0.0132

Gnomad AMR exome

AF:

0.0243

Gnomad ASJ exome

AF:

0.0200

Gnomad EAS exome

AF:

0.0239

Gnomad SAS exome

AF:

0.0169

Gnomad FIN exome

AF:

0.0297

Gnomad NFE exome

AF:

0.0327

Gnomad OTH exome

AF:

0.0360

GnomAD4 exome

AF:

0.0196

AC:

10546

AN:

538964

Hom.:

Cov.:

AF XY:

0.00667

AC XY:

1018

AN XY:

152590

show subpopulations

Gnomad4 AFR exome

AF:

0.00694

Gnomad4 AMR exome

AF:

0.0170

Gnomad4 ASJ exome

AF:

0.0114

Gnomad4 EAS exome

AF:

0.00690

Gnomad4 SAS exome

AF:

0.00820

Gnomad4 FIN exome

AF:

0.0536

Gnomad4 NFE exome

AF:

0.0199

Gnomad4 OTH exome

AF:

0.0203

GnomAD4 genome

AF:

0.0369

AC:

1365

AN:

37008

Hom.:

Cov.:

AF XY:

0.00997

AC XY:

AN XY:

7122

show subpopulations

Gnomad4 AFR

AF:

0.0116

Gnomad4 AMR

AF:

0.0330

Gnomad4 ASJ

AF:

0.0180

Gnomad4 EAS

AF:

0.0141

Gnomad4 SAS

AF:

0.00931

Gnomad4 FIN

AF:

0.0790

Gnomad4 NFE

AF:

0.0508

Gnomad4 OTH

AF:

0.0424

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 08, 2019	- -

Developmental and epileptic encephalopathy, 36

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Dec 05, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

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