5-10981586-A-AACACAC

Position:

• chr5-10981586-A-AACACAC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001332.4(CTNND2):​c.3417+181_3417+186dupGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.10 (849 hom., cov: 20)
• Consequence: CTNND2 NM_001332.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.53

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]

CTNND2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-10981586-A-AACACAC is Benign according to our data. Variant chr5-10981586-A-AACACAC is described in ClinVar as [Benign]. Clinvar id is 1183085.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNND2	NM_001332.4	c.3417+181_3417+186dupGTGTGT		intron_variant		ENST00000304623.13	NP_001323.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTNND2	ENST00000304623.13	c.3417+181_3417+186dupGTGTGT		intron_variant		1	NM_001332.4	ENSP00000307134.8

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15255 AN: 150276 Hom.: 848 Cov.: 20

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0764

Gnomad ASJ AF: 0.0831

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.0703

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.0899

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

GnomAD4 genome AF: 0.102 AC: 15268 AN: 150384 Hom.: 849 Cov.: 20 AF XY: 0.0999 AC XY: 7331 AN XY: 73394

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0770

Gnomad4 ASJ AF: 0.0831

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.0698

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.0836

Gnomad4 OTH AF: 0.0899

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 19, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs112742699; hg19: chr5-10981698;