11-83578951-A-G

Position:

• chr11-83578951-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.1941-37093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,014 control chromosomes in the GnomAD database, including 17,919 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 0.48 (17919 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

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]

DLG2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLG2	NM_001142699.3	c.1941-37093T>C		intron_variant		ENST00000376104.7	NP_001136171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLG2	ENST00000376104.7	c.1941-37093T>C		intron_variant		1	NM_001142699.3	ENSP00000365272.2

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72407 AN: 151894 Hom.: 17882 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.477 AC: 72497 AN: 152014 Hom.: 17919 Cov.: 32 AF XY: 0.479 AC XY: 35598 AN XY: 74298

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.471

Alfa AF: 0.424 Hom.: 24959

Bravo AF: 0.495

Asia WGS AF: 0.531 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.46

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: rs535809; hg19: chr11-83289994;