rs13189742

Positions:

• chr5-11041675-A-C
• chr5-11041675-A-G

Variant summary

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

The NM_001332.4(CTNND2):​c.2789-18696T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0759 in 152,198 control chromosomes in the GnomAD database, including 563 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 0.076 (563 hom., cov: 32)
• Consequence: CTNND2 NM_001332.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNND2	NM_001332.4	c.2789-18696T>G		intron_variant		ENST00000304623.13	NP_001323.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTNND2	ENST00000304623.13	c.2789-18696T>G		intron_variant		1	NM_001332.4	ENSP00000307134	P1

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 11545 AN: 152078 Hom.: 559 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0730

Gnomad ASJ AF: 0.0678

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0779

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

GnomAD4 genome AF: 0.0759 AC: 11558 AN: 152198 Hom.: 563 Cov.: 32 AF XY: 0.0768 AC XY: 5711 AN XY: 74400

Gnomad4 AFR AF: 0.0187

Gnomad4 AMR AF: 0.0730

Gnomad4 ASJ AF: 0.0678

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.0334 Hom.: 34

Bravo AF: 0.0677

Asia WGS AF: 0.0640 AC: 224 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
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: rs13189742; hg19: chr5-11041787;