11-83915935-A-C

Position:

• chr11-83915935-A-C

Variant summary

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

The NM_001142699.3(DLG2):​c.1496+14393T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,114 control chromosomes in the GnomAD database, including 53,410 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 0.84 (53410 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

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]

LOC124902729 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLG2	NM_001142699.3	c.1496+14393T>G		intron_variant		ENST00000376104.7
LOC124902729	XR_007062821.1	n.83-2962A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLG2	ENST00000376104.7	c.1496+14393T>G		intron_variant		1	NM_001142699.3

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126966 AN: 151998 Hom.: 53360 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.835 AC: 127073 AN: 152114 Hom.: 53410 Cov.: 32 AF XY: 0.836 AC XY: 62123 AN XY: 74350

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.824

Alfa AF: 0.808 Hom.: 22689

Bravo AF: 0.838

Asia WGS AF: 0.899 AC: 3127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.8
DANN	Benign	0.77

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: rs790361; hg19: chr11-83626978;