rs1270912

chr10-77838130-A-G

Variant summary

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

The NM_004747.4(DLG5):c.1438-2208T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,134 control chromosomes in the GnomAD database, including 41,186 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 0.73 (41186 hom., cov: 33)
• Consequence: DLG5 NM_004747.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

DLG5 (HGNC:2904): (discs large MAGUK scaffold protein 5) This gene encodes a member of the family of discs large (DLG) homologs, a subset of the membrane-associated guanylate kinase (MAGUK) superfamily. The MAGUK proteins are composed of a catalytically inactive guanylate kinase domain, in addition to PDZ and SH3 domains, and are thought to function as scaffolding molecules at sites of cell-cell contact. The protein encoded by this gene localizes to the plasma membrane and cytoplasm, and interacts with components of adherens junctions and the cytoskeleton. It is proposed to function in the transmission of extracellular signals to the cytoskeleton and in the maintenance of epithelial cell structure. Alternative splice variants have been described but their biological nature has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLG5	NM_004747.4	c.1438-2208T>C		intron_variant		ENST00000372391.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLG5	ENST00000372391.7	c.1438-2208T>C		intron_variant		1	NM_004747.4	P1
DLG5	ENST00000468332.6	c.*795-2208T>C		intron_variant, NMD_transcript_variant		2
DLG5	ENST00000475613.6	n.94-7257T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110868 AN: 152016 Hom.: 41140 Cov.: 33

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.729 AC: 110972 AN: 152134 Hom.: 41186 Cov.: 33 AF XY: 0.726 AC XY: 54000 AN XY: 74356

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.709

Alfa AF: 0.708 Hom.: 6129

Bravo AF: 0.747

Asia WGS AF: 0.766 AC: 2663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.62
Dann	Benign	0.85

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: rs1270912; hg19: chr10-79597888;