11-83615936-C-T

Variant names:

• chr11-83615936-C-T
• rs489567
• NM_001142699.3:c.1940+17275G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142699.3(DLG2):​c.1940+17275G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,124 control chromosomes in the GnomAD database, including 34,879 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 0.67 (34879 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLG2	NM_001142699.3	c.1940+17275G>A		intron_variant	Intron 19 of 27	ENST00000376104.7	NP_001136171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLG2	ENST00000376104.7	c.1940+17275G>A		intron_variant	Intron 19 of 27	1	NM_001142699.3	ENSP00000365272.2

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102109 AN: 152006 Hom.: 34820 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.672 AC: 102232 AN: 152124 Hom.: 34879 Cov.: 32 AF XY: 0.677 AC XY: 50334 AN XY: 74356

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.646

Alfa AF: 0.605 Hom.: 45083

Bravo AF: 0.675

Asia WGS AF: 0.689 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.17

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

Publications

LitVar

Other links and lift over

dbSNP: rs489567; hg19: chr11-83326979;