rs2155413

Variant names:

• chr11-84923746-C-A
• rs2155413
• NM_001142699.3:c.357+187915G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-84923746-C-A
• chr11-84923746-C-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.357+187915G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,790 control chromosomes in the GnomAD database, including 24,866 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 0.55 (24866 hom., cov: 30)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.820
• Publications: 18 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLG2	NM_001142699.3	MANE Select	c.357+187915G>T		intron	N/A	NP_001136171.1
	DLG2	NM_001351274.2		c.393+230810G>T		intron	N/A	NP_001338203.1
	DLG2	NM_001351275.2		c.393+230810G>T		intron	N/A	NP_001338204.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLG2	ENST00000376104.7	TSL:1 MANE Select	c.357+187915G>T		intron	N/A	ENSP00000365272.2
	DLG2	ENST00000650630.1		c.468+187915G>T		intron	N/A	ENSP00000497771.1
	DLG2	ENST00000706226.1		c.393+230810G>T		intron	N/A	ENSP00000516284.1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84112 AN: 151670 Hom.: 24833 Cov.: 30

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.555 AC: 84199 AN: 151790 Hom.: 24866 Cov.: 30 AF XY: 0.552 AC XY: 40965 AN XY: 74194

African (AFR) AF: 0.738 AC: 30562 AN: 41388

American (AMR) AF: 0.564 AC: 8612 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1596 AN: 3466

East Asian (EAS) AF: 0.823 AC: 4231 AN: 5142

South Asian (SAS) AF: 0.546 AC: 2624 AN: 4806

European-Finnish (FIN) AF: 0.330 AC: 3484 AN: 10544

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31213 AN: 67882

Other (OTH) AF: 0.575 AC: 1207 AN: 2100

Alfa AF: 0.501 Hom.: 63582

Bravo AF: 0.585

Asia WGS AF: 0.693 AC: 2413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.42
PhyloP100		0.82
PromoterAI		-0.013	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2155413; hg19: chr11-84634790;