rs4143314

chr11-83780452-T-Cchr11-83780452-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142699.3(DLG2):c.1825+6238A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,050 control chromosomes in the GnomAD database, including 11,748 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 0.39 (11748 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.922

Genes affected

DLG2 (HGNC:2901): (discs large MAGUK scaffold protein 2) This gene encodes a member of the membrane-associated guanylate kinase (MAGUK) family. The encoded protein forms a heterodimer with a related family member that may interact at postsynaptic sites to form a multimeric scaffold for the clustering of receptors, ion channels, and associated signaling proteins. Multiple transcript variants encoding different isoforms have been found for this gene. Additional transcript variants have been described, but their full-length nature is not known. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLG2	NM_001142699.3	c.1825+6238A>G		intron_variant		ENST00000376104.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLG2	ENST00000376104.7	c.1825+6238A>G		intron_variant		1	NM_001142699.3

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58942 AN: 151932 Hom.: 11751 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.388 AC: 58955 AN: 152050 Hom.: 11748 Cov.: 32 AF XY: 0.387 AC XY: 28806 AN XY: 74342

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.423

Alfa AF: 0.396 Hom.: 2095

Bravo AF: 0.379

Asia WGS AF: 0.358 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	8.8
Dann	Benign	0.81

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

Other links and lift over

dbSNP: rs4143314; hg19: chr11-83491495;