11-83667023-C-T

Variant names:

• chr11-83667023-C-T
• rs7928379
• NM_001142699.3:c.1826-33698G>A

Variant summary

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

The NM_001142699.3(DLG2):​c.1826-33698G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,064 control chromosomes in the GnomAD database, including 16,832 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 0.45 (16832 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 3 publications found

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-AS2 (HGNC:40179): (DLG2 antisense RNA 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLG2	NM_001142699.3	c.1826-33698G>A		intron_variant	Intron 18 of 27	ENST00000376104.7	NP_001136171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLG2	ENST00000376104.7	c.1826-33698G>A		intron_variant	Intron 18 of 27	1	NM_001142699.3	ENSP00000365272.2

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67793 AN: 151948 Hom.: 16795 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.446 AC: 67874 AN: 152064 Hom.: 16832 Cov.: 32 AF XY: 0.446 AC XY: 33127 AN XY: 74308

African (AFR) AF: 0.669 AC: 27758 AN: 41492

American (AMR) AF: 0.253 AC: 3873 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1227 AN: 5178

South Asian (SAS) AF: 0.431 AC: 2074 AN: 4814

European-Finnish (FIN) AF: 0.463 AC: 4883 AN: 10540

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25103 AN: 67972

Other (OTH) AF: 0.415 AC: 878 AN: 2114

Alfa AF: 0.312 Hom.: 1231

Bravo AF: 0.436

Asia WGS AF: 0.339 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.43
DANN	Benign	0.52
PhyloP100		-1.6
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: rs7928379; hg19: chr11-83378066;