rs10513097

chr5-11352989-A-Gchr5-11352989-A-T

Variant summary

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

The NM_001332.4(CTNND2):c.1373-6362T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,488 control chromosomes in the GnomAD database, including 3,856 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 0.22 (3856 hom., cov: 31)
• Consequence: CTNND2 NM_001332.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

CTNND2 (HGNC:2516): (catenin delta 2) This gene encodes an adhesive junction associated protein of the armadillo/beta-catenin superfamily and is implicated in brain and eye development and cancer formation. The protein encoded by this gene promotes the disruption of E-cadherin based adherens junction to favor cell spreading upon stimulation by hepatocyte growth factor. This gene is overexpressed in prostate adenocarcinomas and is associated with decreased expression of tumor suppressor E-cadherin in this tissue. This gene resides in a region of the short arm of chromosome 5 that is deleted in Cri du Chat syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNND2	NM_001332.4	c.1373-6362T>C		intron_variant		ENST00000304623.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNND2	ENST00000304623.13	c.1373-6362T>C		intron_variant		1	NM_001332.4	P1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 32939 AN: 151398 Hom.: 3847 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.218 AC: 32964 AN: 151488 Hom.: 3856 Cov.: 31 AF XY: 0.224 AC XY: 16582 AN XY: 73946

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.240

Alfa AF: 0.217 Hom.: 1920

Bravo AF: 0.212

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.85
Dann	Benign	0.34

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: rs10513097; hg19: chr5-11353101;