chr11-84894629-G-A

Position:

• chr11-84894629-G-A

Variant summary

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

The NM_001142699.3(DLG2):​c.357+217032C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,956 control chromosomes in the GnomAD database, including 13,873 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 0.42 (13873 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLG2	NM_001142699.3	c.357+217032C>T		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+217032C>T		intron_variant		1	NM_001142699.3	ENSP00000365272

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63785 AN: 151838 Hom.: 13858 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.420 AC: 63835 AN: 151956 Hom.: 13873 Cov.: 32 AF XY: 0.424 AC XY: 31514 AN XY: 74268

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.412

Alfa AF: 0.414 Hom.: 6766

Bravo AF: 0.399

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.29

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: rs6592211; hg19: chr11-84605673;