11-83730219-C-T

Variant names:

• chr11-83730219-C-T
• rs7104950
• NM_001142699.3:c.1825+56471G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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):

• neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• delayed puberty, self-limited

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142699.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLG2	NM_001142699.3	MANE Select	c.1825+56471G>A		intron	N/A	NP_001136171.1	Q15700-2
	DLG2	NM_001351274.2		c.1861+56471G>A		intron	N/A	NP_001338203.1	A0A994J819
	DLG2	NM_001351275.2		c.1858+56471G>A		intron	N/A	NP_001338204.1	A0A994J7P1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLG2	ENST00000376104.7	TSL:1 MANE Select	c.1825+56471G>A		intron	N/A	ENSP00000365272.2	Q15700-2
	DLG2	ENST00000398309.6	TSL:1	c.1510+56471G>A		intron	N/A	ENSP00000381355.2	Q15700-1
	DLG2	ENST00000532653.5	TSL:1	c.1510+56471G>A		intron	N/A	ENSP00000435849.1	B7Z2T4

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

African (AFR) AF: 0.587 AC: 22917 AN: 39050

American (AMR) AF: 0.205 AC: 2627 AN: 12836

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 791 AN: 3394

East Asian (EAS) AF: 0.150 AC: 673 AN: 4490

South Asian (SAS) AF: 0.272 AC: 1196 AN: 4396

European-Finnish (FIN) AF: 0.355 AC: 2843 AN: 8018

Middle Eastern (MID) AF: 0.250 AC: 59 AN: 236

European-Non Finnish (NFE) AF: 0.219 AC: 14325 AN: 65460

Other (OTH) AF: 0.282 AC: 553 AN: 1962

Alfa AF: 0.164 Hom.: 397

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.48
PhyloP100		-0.92
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: rs7104950; hg19: chr11-83441262;