chr11-83879838-A-G

Position:

• chr11-83879838-A-G

Variant summary

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

The NM_001142699.3(DLG2):​c.1497-5350T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,074 control chromosomes in the GnomAD database, including 13,361 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 0.41 (13361 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLG2	NM_001142699.3	c.1497-5350T>C		intron_variant		ENST00000376104.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLG2	ENST00000376104.7	c.1497-5350T>C		intron_variant		1	NM_001142699.3

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62564 AN: 151956 Hom.: 13350 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.412 AC: 62623 AN: 152074 Hom.: 13361 Cov.: 32 AF XY: 0.413 AC XY: 30697 AN XY: 74348

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.400

Alfa AF: 0.384 Hom.: 1441

Bravo AF: 0.409

Asia WGS AF: 0.480 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.79

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: rs10751099; hg19: chr11-83590881;