rs790361

Variant names:

• chr11-83915935-A-C
• rs790361
• NM_001142699.3:c.1496+14393T>G

Variant summary

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

The NM_001142699.3(DLG2):​c.1496+14393T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,114 control chromosomes in the GnomAD database, including 53,410 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 0.84 (53410 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 1 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 Gene-Disease associations (from GenCC):

• delayed puberty, self-limited

  Inheritance: AD, AR Classification: LIMITED Submitted by: Ambry Genetics
• neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

LOC124902729 (HGNC:):

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 = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLG2	NM_001142699.3	c.1496+14393T>G		intron_variant	Intron 15 of 27	ENST00000376104.7	NP_001136171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLG2	ENST00000376104.7	c.1496+14393T>G		intron_variant	Intron 15 of 27	1	NM_001142699.3	ENSP00000365272.2

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126966 AN: 151998 Hom.: 53360 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.835 AC: 127073 AN: 152114 Hom.: 53410 Cov.: 32 AF XY: 0.836 AC XY: 62123 AN XY: 74350

African (AFR) AF: 0.930 AC: 38643 AN: 41540

American (AMR) AF: 0.763 AC: 11633 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2906 AN: 3470

East Asian (EAS) AF: 0.911 AC: 4709 AN: 5168

South Asian (SAS) AF: 0.904 AC: 4352 AN: 4816

European-Finnish (FIN) AF: 0.782 AC: 8253 AN: 10556

Middle Eastern (MID) AF: 0.815 AC: 238 AN: 292

European-Non Finnish (NFE) AF: 0.792 AC: 53885 AN: 68000

Other (OTH) AF: 0.824 AC: 1740 AN: 2112

Alfa AF: 0.808 Hom.: 25487

Bravo AF: 0.838

Asia WGS AF: 0.899 AC: 3127 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	5.8
DANN	Benign	0.77
PhyloP100		0.085
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: rs790361; hg19: chr11-83626978;