rs17807611

chr11-84527856-G-Cchr11-84527856-G-T

Variant summary

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

The NM_001142699.3(DLG2):c.519+6714C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 148,710 control chromosomes in the GnomAD database, including 594 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 0.087 (594 hom., cov: 31)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLG2	NM_001142699.3	c.519+6714C>G		intron_variant		ENST00000376104.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLG2	ENST00000376104.7	c.519+6714C>G		intron_variant		1	NM_001142699.3

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 12930 AN: 148594 Hom.: 595 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0188

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0607

Gnomad EAS AF: 0.0485

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.0719

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.0812

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

GnomAD4 genome AF: 0.0871 AC: 12949 AN: 148710 Hom.: 594 Cov.: 31 AF XY: 0.0871 AC XY: 6294 AN XY: 72272

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0535

Gnomad4 ASJ AF: 0.0607

Gnomad4 EAS AF: 0.0486

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0484

Gnomad4 NFE AF: 0.0786

Gnomad4 OTH AF: 0.0804

Alfa AF: 0.0263 Hom.: 18

Bravo AF: 0.0866

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.6
Dann	Benign	0.41

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: rs17807611; hg19: chr11-84238899;