Variant X-111744768-ACCTCCTCCTCCTCCTCCTCCTCCT-ACCTCCTCCTCCTCCTCCT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_001099922.3(ALG13):c.2830_2835delCCTCCT(p.Pro944_Pro945del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 591,212 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 209 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0019 ( 0 hom., 7 hem., cov: 9)

Exomes 𝑓: 0.0014 ( 0 hom. 202 hem. )

Consequence

ALG13
NM_001099922.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:2

Conservation

PhyloP100: 0.116

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 -9 ACMG points.

BP6

Variant X-111744768-ACCTCCT-A is Benign according to our data. Variant chrX-111744768-ACCTCCT-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 238294.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1, Benign=1}.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00194 (72/37153) while in subpopulation SAS AF= 0.00559 (3/537). AF 95% confidence interval is 0.002. There are 0 homozygotes in gnomad4. There are 7 alleles in male gnomad4 subpopulation. Median coverage is 9. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd4 at 7 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALG13	NM_001099922.3 linkuse as main transcript	c.2830_2835delCCTCCT	p.Pro944_Pro945del	conservative_inframe_deletion	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.2830_2835delCCTCCT	p.Pro944_Pro945del	conservative_inframe_deletion	24/27	2	NM_001099922.3	ENSP00000378260.3		Q9NP73-1

Frequencies

GnomAD3 genomes

AF:

0.00194

AC:

AN:

37157

Hom.:

Cov.:

AF XY:

0.000980

AC XY:

AN XY:

7145

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00160

Gnomad ASJ

AF:

0.000998

Gnomad EAS

AF:

0.000828

Gnomad SAS

AF:

0.00556

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00256

Gnomad OTH

AF:

0.00471

GnomAD3 exomes

AF:

0.00313

AC:

104

AN:

33243

Hom.:

AF XY:

0.00406

AC XY:

AN XY:

5669

show subpopulations

Gnomad AFR exome

AF:

0.00214

Gnomad AMR exome

AF:

0.00465

Gnomad ASJ exome

AF:

0.00193

Gnomad EAS exome

AF:

0.00227

Gnomad SAS exome

AF:

0.00724

Gnomad FIN exome

AF:

0.00156

Gnomad NFE exome

AF:

0.00213

Gnomad OTH exome

AF:

0.00300

GnomAD4 exome

AF:

0.00137

AC:

757

AN:

554059

Hom.:

AF XY:

0.00129

AC XY:

202

AN XY:

156805

show subpopulations

Gnomad4 AFR exome

AF:

0.00182

Gnomad4 AMR exome

AF:

0.00226

Gnomad4 ASJ exome

AF:

0.00201

Gnomad4 EAS exome

AF:

0.00150

Gnomad4 SAS exome

AF:

0.00386

Gnomad4 FIN exome

AF:

0.000378

Gnomad4 NFE exome

AF:

0.00119

Gnomad4 OTH exome

AF:

0.00152

GnomAD4 genome

AF:

0.00194

AC:

AN:

37153

Hom.:

Cov.:

AF XY:

0.000980

AC XY:

AN XY:

7145

show subpopulations

Gnomad4 AFR

AF:

0.00101

Gnomad4 AMR

AF:

0.00159

Gnomad4 ASJ

AF:

0.000998

Gnomad4 EAS

AF:

0.000828

Gnomad4 SAS

AF:

0.00559

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00256

Gnomad4 OTH

AF:

0.00466

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:2

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy, 36

Uncertain:1Benign:1

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Dec 18, 2017	- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2024

ALG13: BS2 -

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