NM_133642.5:c.435C>T

Variant names:

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_133642.5(LARGE1):c.435C>T(p.Ala145Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,612,472 control chromosomes in the GnomAD database, including 194,473 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 14560 hom., cov: 32)

Exomes 𝑓: 0.49 ( 179913 hom. )

Consequence

LARGE1
NM_133642.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: -0.0540

Variant links:

Genes affected

LARGE1 (HGNC:6511): (LARGE xylosyl- and glucuronyltransferase 1) This gene encodes a member of the N-acetylglucosaminyltransferase gene family. It encodes a glycosyltransferase which participates in glycosylation of alpha-dystroglycan, and may carry out the synthesis of glycoprotein and glycosphingolipid sugar chains. It may also be involved in the addition of a repeated disaccharide unit. The protein encoded by this gene is the glycotransferase that adds the final xylose and glucuronic acid to alpha-dystroglycan and thereby allows alpha-dystroglycan to bind ligands including laminin 211 and neurexin. Mutations in this gene cause several forms of congenital muscular dystrophy characterized by cognitive disability and abnormal glycosylation of alpha-dystroglycan. Alternative splicing of this gene results in multiple transcript variants that encode the same protein. [provided by RefSeq, May 2018]

LARGE1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BP6

Variant 22-33626300-G-A is Benign according to our data. Variant chr22-33626300-G-A is described in ClinVar as [Benign]. Clinvar id is 95175.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-33626300-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.054 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LARGE1	NM_133642.5 link	c.435C>T	p.Ala145Ala	synonymous_variant	Exon 4 of 15	ENST00000397394.8	NP_598397.1	O95461-1X5DR28

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LARGE1	ENST00000397394.8 link	c.435C>T	p.Ala145Ala	synonymous_variant	Exon 4 of 15	5	NM_133642.5	ENSP00000380549.2		O95461-1

Frequencies

GnomAD3 genomes

AF:

0.408

AC:

62024

AN:

151924

Hom.:

14551

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.522

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.537

Gnomad EAS

AF:

0.584

Gnomad SAS

AF:

0.518

Gnomad FIN

AF:

0.524

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.490

Gnomad OTH

AF:

0.436

GnomAD3 exomes

AF:

0.488

AC:

122435

AN:

251030

Hom.:

30948

AF XY:

0.492

AC XY:

66673

AN XY:

135640

show subpopulations

Gnomad AFR exome

AF:

0.154

Gnomad AMR exome

AF:

0.542

Gnomad ASJ exome

AF:

0.542

Gnomad EAS exome

AF:

0.572

Gnomad SAS exome

AF:

0.507

Gnomad FIN exome

AF:

0.525

Gnomad NFE exome

AF:

0.488

Gnomad OTH exome

AF:

0.501

GnomAD4 exome

AF:

0.492

AC:

718511

AN:

1460430

Hom.:

179913

Cov.:

AF XY:

0.493

AC XY:

358346

AN XY:

726612

show subpopulations

Gnomad4 AFR exome

AF:

0.150

Gnomad4 AMR exome

AF:

0.533

Gnomad4 ASJ exome

AF:

0.542

Gnomad4 EAS exome

AF:

0.595

Gnomad4 SAS exome

AF:

0.511

Gnomad4 FIN exome

AF:

0.522

Gnomad4 NFE exome

AF:

0.493

Gnomad4 OTH exome

AF:

0.488

GnomAD4 genome

AF:

0.408

AC:

62037

AN:

152042

Hom.:

14560

Cov.:

AF XY:

0.411

AC XY:

30510

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.497

Gnomad4 ASJ

AF:

0.537

Gnomad4 EAS

AF:

0.584

Gnomad4 SAS

AF:

0.518

Gnomad4 FIN

AF:

0.524

Gnomad4 NFE

AF:

0.490

Gnomad4 OTH

AF:

0.440

Alfa

AF:

0.451

Hom.:

12597

Bravo

AF:

0.398

Asia WGS

AF:

0.518

AC:

1802

AN:

3478

EpiCase

AF:

0.507

EpiControl

AF:

0.506

ClinVar

Significance: Benign

Submissions summary: Benign:12

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 13, 2012

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:3

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 07, 2018

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Muscular dystrophy-dystroglycanopathy type B6

Benign:2

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A6

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Benign

0.79

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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