rs1451397

Variant names:

• chr11-83700550-C-T
• rs1451397
• NM_001142699.3:c.1826-67225G>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.1826-67225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 151,976 control chromosomes in the GnomAD database, including 6,875 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 0.27 (6875 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• 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-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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLG2	NM_001142699.3	c.1826-67225G>A		intron_variant	Intron 18 of 27	ENST00000376104.7	NP_001136171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLG2	ENST00000376104.7	c.1826-67225G>A		intron_variant	Intron 18 of 27	1	NM_001142699.3	ENSP00000365272.2

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41099 AN: 151858 Hom.: 6851 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.271 AC: 41162 AN: 151976 Hom.: 6875 Cov.: 32 AF XY: 0.273 AC XY: 20300 AN XY: 74278

African (AFR) AF: 0.471 AC: 19502 AN: 41412

American (AMR) AF: 0.149 AC: 2269 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3462

East Asian (EAS) AF: 0.148 AC: 765 AN: 5174

South Asian (SAS) AF: 0.239 AC: 1153 AN: 4820

European-Finnish (FIN) AF: 0.301 AC: 3166 AN: 10528

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12749 AN: 67992

Other (OTH) AF: 0.234 AC: 493 AN: 2110

Alfa AF: 0.200 Hom.: 5809

Bravo AF: 0.265

Asia WGS AF: 0.215 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.33
DANN	Benign	0.61
PhyloP100		-1.3
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: rs1451397; hg19: chr11-83411593;