Variant rs13440710 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001099922.3(ALG13):c.2799T>A(p.Pro933=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P933P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0050 ( 0 hom., 1 hem., cov: 9)

Exomes 𝑓: 0.0050 ( 0 hom. 72 hem. )

Consequence

ALG13
NM_001099922.3 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.799

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant X-111744771-T-A is Benign according to our data. Variant chrX-111744771-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 412611.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111744771-T-A is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-0.799 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00504 (223/44251) while in subpopulation AFR AF= 0.0161 (158/9830). AF 95% confidence interval is 0.014. There are 0 homozygotes in gnomad4. There are 1 alleles in male gnomad4 subpopulation. Median coverage is 9. This position pass quality control queck.

BS2

High Hemizygotes in GnomAdExome4 at 72 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALG13	NM_001099922.3 linkuse as main transcript	c.2799T>A	p.Pro933=	synonymous_variant	24/27	ENST00000394780.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALG13	ENST00000394780.8 linkuse as main transcript	c.2799T>A	p.Pro933=	synonymous_variant	24/27	2	NM_001099922.3	A2	Q9NP73-1

Frequencies

GnomAD3 genomes

AF:

0.00504

AC:

223

AN:

44241

Hom.:

Cov.:

AF XY:

0.000114

AC XY:

AN XY:

8749

show subpopulations

Gnomad AFR

AF:

0.0161

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00312

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00642

Gnomad SAS

AF:

0.0117

Gnomad FIN

AF:

0.00480

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00114

Gnomad OTH

AF:

0.00541

GnomAD3 exomes

AF:

0.00296

AC:

AN:

28366

Hom.:

AF XY:

0.00

AC XY:

AN XY:

4998

show subpopulations

Gnomad AFR exome

AF:

0.0105

Gnomad AMR exome

AF:

0.00146

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00524

Gnomad SAS exome

AF:

0.00840

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00115

Gnomad OTH exome

AF:

0.00331

GnomAD4 exome

AF:

0.00501

AC:

1089

AN:

217287

Hom.:

Cov.:

AF XY:

0.00120

AC XY:

AN XY:

59767

show subpopulations

Gnomad4 AFR exome

AF:

0.0280

Gnomad4 AMR exome

AF:

0.00490

Gnomad4 ASJ exome

AF:

0.00134

Gnomad4 EAS exome

AF:

0.0433

Gnomad4 SAS exome

AF:

0.0142

Gnomad4 FIN exome

AF:

0.0124

Gnomad4 NFE exome

AF:

0.00272

Gnomad4 OTH exome

AF:

0.00672

GnomAD4 genome

AF:

0.00504

AC:

223

AN:

44251

Hom.:

Cov.:

AF XY:

0.000114

AC XY:

AN XY:

8753

show subpopulations

Gnomad4 AFR

AF:

0.0161

Gnomad4 AMR

AF:

0.00311

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00641

Gnomad4 SAS

AF:

0.0118

Gnomad4 FIN

AF:

0.00480

Gnomad4 NFE

AF:

0.00114

Gnomad4 OTH

AF:

0.00534

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy, 36

Benign:3

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Dec 05, 2021	- -
Likely benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Dec 01, 2021	- -
Likely benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Jun 23, 2020

- -

ALG13-related disorder

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 07, 2019

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 16, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.61

DANN

Benign

0.39

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