rs10751099

Variant names:

• chr11-83879838-A-G
• rs10751099
• NM_001142699.3:c.1497-5350T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-83879838-A-G
• chr11-83879838-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142699.3(DLG2):​c.1497-5350T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,074 control chromosomes in the GnomAD database, including 13,361 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 0.41 (13361 hom., cov: 32)
• Consequence: DLG2 NM_001142699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 1 publications found

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]

DLG2 Gene-Disease associations (from GenCC):

• delayed puberty, self-limited

  Inheritance: AD, AR Classification: LIMITED Submitted by: Ambry Genetics
• neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLG2	NM_001142699.3	c.1497-5350T>C		intron_variant	Intron 15 of 27	ENST00000376104.7	NP_001136171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLG2	ENST00000376104.7	c.1497-5350T>C		intron_variant	Intron 15 of 27	1	NM_001142699.3	ENSP00000365272.2

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62564 AN: 151956 Hom.: 13350 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.412 AC: 62623 AN: 152074 Hom.: 13361 Cov.: 32 AF XY: 0.413 AC XY: 30697 AN XY: 74348

African (AFR) AF: 0.498 AC: 20647 AN: 41482

American (AMR) AF: 0.335 AC: 5116 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1453 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2210 AN: 5174

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4816

European-Finnish (FIN) AF: 0.374 AC: 3950 AN: 10572

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.372 AC: 25288 AN: 67980

Other (OTH) AF: 0.400 AC: 845 AN: 2112

Alfa AF: 0.388 Hom.: 1534

Bravo AF: 0.409

Asia WGS AF: 0.480 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		-0.052
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10751099; hg19: chr11-83590881;