rs1823777

Positions:

• chr11-85075167-C-A
• chr11-85075167-C-T

Variant summary

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

The NM_001142699.3(DLG2):​c.357+36494G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 151,748 control chromosomes in the GnomAD database, including 4,655 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 0.24 (4655 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLG2	NM_001142699.3	c.357+36494G>T		intron_variant		ENST00000376104.7	NP_001136171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLG2	ENST00000376104.7	c.357+36494G>T		intron_variant		1	NM_001142699.3	ENSP00000365272.2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36530 AN: 151630 Hom.: 4644 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.241 AC: 36560 AN: 151748 Hom.: 4655 Cov.: 32 AF XY: 0.242 AC XY: 17928 AN XY: 74138

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.0500

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.238

Alfa AF: 0.186 Hom.: 522

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
DANN	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1823777; hg19: chr11-84786211;