rs1400316

Variant names:

• chr11-83875794-A-G
• rs1400316
• NM_001142699.3:c.1497-1306T>C

Variant summary

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

The NM_001142699.3(DLG2):​c.1497-1306T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,982 control chromosomes in the GnomAD database, including 11,707 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 0.39 (11707 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 6 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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLG2	NM_001142699.3	c.1497-1306T>C		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.1497-1306T>C		intron_variant	Intron 15 of 27	1	NM_001142699.3	ENSP00000365272.2

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59167 AN: 151866 Hom.: 11699 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.390 AC: 59214 AN: 151982 Hom.: 11707 Cov.: 32 AF XY: 0.389 AC XY: 28907 AN XY: 74290

African (AFR) AF: 0.407 AC: 16893 AN: 41470

American (AMR) AF: 0.323 AC: 4920 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1310 AN: 3468

East Asian (EAS) AF: 0.402 AC: 2072 AN: 5158

South Asian (SAS) AF: 0.520 AC: 2504 AN: 4816

European-Finnish (FIN) AF: 0.383 AC: 4038 AN: 10550

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.388 AC: 26398 AN: 67954

Other (OTH) AF: 0.378 AC: 797 AN: 2108

Alfa AF: 0.390 Hom.: 36583

Bravo AF: 0.384

Asia WGS AF: 0.425 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.82
PhyloP100		-0.069
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: rs1400316; hg19: chr11-83586837;