rs10898278

chr11-84622198-T-C

Variant summary

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

The NM_001142699.3(DLG2):c.358-87467A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,164 control chromosomes in the GnomAD database, including 1,576 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 0.12 (1576 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLG2	NM_001142699.3	c.358-87467A>G		intron_variant		ENST00000376104.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLG2	ENST00000376104.7	c.358-87467A>G		intron_variant		1	NM_001142699.3

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18858 AN: 152046 Hom.: 1567 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0706

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0537

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.124 AC: 18893 AN: 152164 Hom.: 1576 Cov.: 32 AF XY: 0.122 AC XY: 9091 AN XY: 74402

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.0704

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0537

Gnomad4 NFE AF: 0.0828

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0952 Hom.: 248

Bravo AF: 0.127

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	12
Dann	Benign	0.79

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: rs10898278; hg19: chr11-84333241;