Variant X-111744768-ACCTCCTCCTCCTCCTCCTCCTCCT-ACCTCCTCCTCCT 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.2824_2835delCCTCCTCCTCCT(p.Pro942_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 0.000456 in 594,412 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 82 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00086 ( 0 hom., 4 hem., cov: 9)

Exomes 𝑓: 0.00043 ( 0 hom. 78 hem. )

Consequence

ALG13
NM_001099922.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.322

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-ACCTCCTCCTCCT-A is Benign according to our data. Variant chrX-111744768-ACCTCCTCCTCCT-A is described in ClinVar as [Likely_benign]. Clinvar id is 516988.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000861 (32/37156) while in subpopulation AMR AF= 0.00278 (7/2520). AF 95% confidence interval is 0.0013. There are 0 homozygotes in gnomad4. There are 4 alleles in male gnomad4 subpopulation. Median coverage is 9. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd4 at 4 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALG13	NM_001099922.3 linkuse as main transcript	c.2824_2835delCCTCCTCCTCCT	p.Pro942_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.2824_2835delCCTCCTCCTCCT	p.Pro942_Pro945del	conservative_inframe_deletion	24/27	2	NM_001099922.3	ENSP00000378260.3		Q9NP73-1

Frequencies

GnomAD3 genomes

AF:

0.000861

AC:

AN:

37160

Hom.:

Cov.:

AF XY:

0.000560

AC XY:

AN XY:

7144

show subpopulations

Gnomad AFR

AF:

0.000101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00279

Gnomad ASJ

AF:

0.00599

Gnomad EAS

AF:

0.00248

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000825

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000703

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000993

AC:

AN:

33243

Hom.:

AF XY:

0.00106

AC XY:

AN XY:

5669

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000957

Gnomad ASJ exome

AF:

0.00451

Gnomad EAS exome

AF:

0.000758

Gnomad SAS exome

AF:

0.00241

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000762

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000429

AC:

239

AN:

557256

Hom.:

AF XY:

0.000492

AC XY:

AN XY:

158534

show subpopulations

Gnomad4 AFR exome

AF:

0.0000692

Gnomad4 AMR exome

AF:

0.000545

Gnomad4 ASJ exome

AF:

0.00347

Gnomad4 EAS exome

AF:

0.00104

Gnomad4 SAS exome

AF:

0.000678

Gnomad4 FIN exome

AF:

0.000377

Gnomad4 NFE exome

AF:

0.000323

Gnomad4 OTH exome

AF:

0.000697

GnomAD4 genome

AF:

0.000861

AC:

AN:

37156

Hom.:

Cov.:

AF XY:

0.000560

AC XY:

AN XY:

7144

show subpopulations

Gnomad4 AFR

AF:

0.000101

Gnomad4 AMR

AF:

0.00278

Gnomad4 ASJ

AF:

0.00599

Gnomad4 EAS

AF:

0.00248

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000825

Gnomad4 NFE

AF:

0.000703

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy, 36

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 27, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Dec 05, 2021	- -

ALG13-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 23, 2021

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

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 12, 2021

- -

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