rs1940078

Positions:

• chr11-84642251-G-C
• chr11-84642251-G-T

Variant summary

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

The NM_001142699.3(DLG2):​c.358-107520C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.934 in 151,414 control chromosomes in the GnomAD database, including 66,113 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 0.93 (66113 hom., cov: 25)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17

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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLG2	NM_001142699.3	c.358-107520C>G		intron_variant		ENST00000376104.7	NP_001136171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLG2	ENST00000376104.7	c.358-107520C>G		intron_variant		1	NM_001142699.3	ENSP00000365272

Frequencies

GnomAD3 genomes AF: 0.934 AC: 141241 AN: 151296 Hom.: 66052 Cov.: 25

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.934 AC: 141361 AN: 151414 Hom.: 66113 Cov.: 25 AF XY: 0.937 AC XY: 69334 AN XY: 73990

Gnomad4 AFR AF: 0.982

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.963

Gnomad4 FIN AF: 0.949

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.936

Alfa AF: 0.895 Hom.: 3356

Bravo AF: 0.934

Asia WGS AF: 0.979 AC: 3400 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.018
DANN	Benign	0.36

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: rs1940078; hg19: chr11-84353294;