5-10981586-A-AAC

Variant summary

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

The NM_001332.4(CTNND2):c.3417+186_3417+187insGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.15 (1594 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]

LOC105374654 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-10981586-A-AAC is Benign according to our data. Variant chr5-10981586-A-AAC is described in ClinVar as [Benign]. Clinvar id is 1253470.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNND2	NM_001332.4	c.3417+186_3417+187insGT		intron_variant		ENST00000304623.13
LOC105374654	XR_925791.3	n.536-2577_536-2576dup		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNND2	ENST00000304623.13	c.3417+186_3417+187insGT		intron_variant		1	NM_001332.4	P1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21810 AN: 150290 Hom.: 1591 Cov.: 20

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.00624

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.145 AC: 21847 AN: 150400 Hom.: 1594 Cov.: 20 AF XY: 0.143 AC XY: 10504 AN XY: 73394

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.00625

Gnomad4 SAS AF: 0.0431

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.151

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

Aug 27, 2019

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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;