chr11-84926021-A-C

Position:

• chr11-84926021-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.357+185640T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,916 control chromosomes in the GnomAD database, including 23,572 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 0.54 (23572 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLG2	NM_001142699.3	c.357+185640T>G		intron_variant		ENST00000376104.7	NP_001136171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLG2	ENST00000376104.7	c.357+185640T>G		intron_variant		1	NM_001142699.3	ENSP00000365272

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81787 AN: 151798 Hom.: 23542 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.539 AC: 81866 AN: 151916 Hom.: 23572 Cov.: 32 AF XY: 0.535 AC XY: 39689 AN XY: 74244

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.565

Alfa AF: 0.506 Hom.: 3908

Bravo AF: 0.569

Asia WGS AF: 0.693 AC: 2405 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.9
DANN	Benign	0.87

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10736767; hg19: chr11-84637065;