NM_133642.5:c.106+10990T>C

Variant names:

• chr22-33750381-A-G
• rs5999086
• NM_133642.5:c.106+10990T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_133642.5(LARGE1):​c.106+10990T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,090 control chromosomes in the GnomAD database, including 6,494 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (6494 hom., cov: 33)
• Consequence: LARGE1 NM_133642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 3 publications found

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]

LARGE-AS1 (HGNC:40336): (LARGE antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_133642.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LARGE1	NM_133642.5	MANE Select	c.106+10990T>C		intron	N/A	NP_598397.1
	LARGE1	NM_001362949.2		c.106+10990T>C		intron	N/A	NP_001349878.1
	LARGE1	NM_001362951.2		c.106+10990T>C		intron	N/A	NP_001349880.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LARGE1	ENST00000397394.8	TSL:5 MANE Select	c.106+10990T>C		intron	N/A	ENSP00000380549.2
	LARGE1	ENST00000354992.7	TSL:1	c.106+10990T>C		intron	N/A	ENSP00000347088.2
	LARGE1	ENST00000402320.6	TSL:1	c.106+10990T>C		intron	N/A	ENSP00000385223.1

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36668 AN: 151972 Hom.: 6469 Cov.: 33

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.213

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.242 AC: 36730 AN: 152090 Hom.: 6494 Cov.: 33 AF XY: 0.236 AC XY: 17566 AN XY: 74364

African (AFR) AF: 0.510 AC: 21131 AN: 41450

American (AMR) AF: 0.141 AC: 2157 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0868 AC: 301 AN: 3468

East Asian (EAS) AF: 0.204 AC: 1052 AN: 5160

South Asian (SAS) AF: 0.0622 AC: 300 AN: 4822

European-Finnish (FIN) AF: 0.135 AC: 1427 AN: 10584

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9756 AN: 67996

Other (OTH) AF: 0.213 AC: 450 AN: 2112

Alfa AF: 0.155 Hom.: 4256

Bravo AF: 0.253

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.68
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5999086; hg19: chr22-34146368;