chr5-11489403-T-C

Position:

• chr5-11489403-T-C

Variant summary

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

The NM_001332.4(CTNND2):​c.287+75541A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,080 control chromosomes in the GnomAD database, including 5,980 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 0.27 (5980 hom., cov: 33)
• Consequence: CTNND2 NM_001332.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

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 (SAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNND2	NM_001332.4	c.287+75541A>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.287+75541A>G		intron_variant		1	NM_001332.4	ENSP00000307134	P1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41497 AN: 151964 Hom.: 5975 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.273 AC: 41525 AN: 152080 Hom.: 5980 Cov.: 33 AF XY: 0.282 AC XY: 20997 AN XY: 74344

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.254

Alfa AF: 0.274 Hom.: 925

Bravo AF: 0.259

Asia WGS AF: 0.267 AC: 928 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	0.57
DANN	Benign	0.76

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: rs32609; hg19: chr5-11489515;