11-83730219-C-T

Position:

• chr11-83730219-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.1825+56471G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 140,726 control chromosomes in the GnomAD database, including 9,262 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 0.33 (9262 hom., cov: 26)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLG2	NM_001142699.3	c.1825+56471G>A		intron_variant		ENST00000376104.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLG2	ENST00000376104.7	c.1825+56471G>A		intron_variant		1	NM_001142699.3

Frequencies

GnomAD3 genomes AF: 0.328 AC: 46152 AN: 140658 Hom.: 9227 Cov.: 26

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.328 AC: 46218 AN: 140726 Hom.: 9262 Cov.: 26 AF XY: 0.333 AC XY: 22473 AN XY: 67424

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.282

Alfa AF: 0.141 Hom.: 277

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.48

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: rs7104950; hg19: chr11-83441262;