NM_001142699.3:c.1826-73393C>A

Variant names:

• chr11-83706718-G-T
• rs10898150
• NM_001142699.3:c.1826-73393C>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.1826-73393C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,084 control chromosomes in the GnomAD database, including 6,361 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 0.26 (6361 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 3 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-AS2 (HGNC:40179): (DLG2 antisense RNA 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 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.1826-73393C>A		intron	N/A	NP_001136171.1
	DLG2	NM_001351274.2		c.1862-73393C>A		intron	N/A	NP_001338203.1
	DLG2	NM_001351275.2		c.1859-73393C>A		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.1826-73393C>A		intron	N/A	ENSP00000365272.2
	DLG2	ENST00000398309.6	TSL:1	c.1511-73393C>A		intron	N/A	ENSP00000381355.2
	DLG2	ENST00000532653.5	TSL:1	c.1511-73393C>A		intron	N/A	ENSP00000435849.1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40224 AN: 151966 Hom.: 6353 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.265 AC: 40264 AN: 152084 Hom.: 6361 Cov.: 32 AF XY: 0.267 AC XY: 19846 AN XY: 74322

African (AFR) AF: 0.443 AC: 18379 AN: 41478

American (AMR) AF: 0.152 AC: 2328 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 777 AN: 3472

East Asian (EAS) AF: 0.136 AC: 700 AN: 5164

South Asian (SAS) AF: 0.238 AC: 1146 AN: 4814

European-Finnish (FIN) AF: 0.300 AC: 3174 AN: 10580

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.191 AC: 12984 AN: 67972

Other (OTH) AF: 0.233 AC: 491 AN: 2110

Alfa AF: 0.167 Hom.: 486

Bravo AF: 0.259

Asia WGS AF: 0.208 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.49
PhyloP100		-0.25
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: rs10898150; hg19: chr11-83417761;