rs7952143

chr11-84456792-G-A

Variant summary

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

The NM_001142699.3(DLG2):c.519+77778C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 150,970 control chromosomes in the GnomAD database, including 15,614 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 (15614 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLG2	NM_001142699.3	c.519+77778C>T		intron_variant		ENST00000376104.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLG2	ENST00000376104.7	c.519+77778C>T		intron_variant		1	NM_001142699.3

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58698 AN: 150852 Hom.: 15564 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.389 AC: 58798 AN: 150970 Hom.: 15614 Cov.: 32 AF XY: 0.377 AC XY: 27801 AN XY: 73784

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.368

Alfa AF: 0.289 Hom.: 9851

Bravo AF: 0.410

Asia WGS AF: 0.340 AC: 1183 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.36

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: rs7952143; hg19: chr11-84167835;