Variant 5-10981767-C-CTTTA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_001332.4(CTNND2):c.3417+5_3417+6insTAAA variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0198 in 1,609,804 control chromosomes in the GnomAD database, including 438 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.017 ( 42 hom., cov: 33)

Exomes 𝑓: 0.020 ( 396 hom. )

Consequence

CTNND2
NM_001332.4 splice_donor_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.479

Variant links:

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 links:

LOC105374654 (HGNC:):

LOC105374654 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-10981767-C-CTTTA is Benign according to our data. Variant chr5-10981767-C-CTTTA is described in ClinVar as [Benign]. Clinvar id is 1292997.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0166 (2526/152256) while in subpopulation NFE AF= 0.0197 (1340/68022). AF 95% confidence interval is 0.0188. There are 42 homozygotes in gnomad4. There are 1367 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High AC in GnomAd at 2519 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNND2	NM_001332.4 linkuse as main transcript	c.3417+5_3417+6insTAAA		splice_donor_region_variant, intron_variant		ENST00000304623.13
LOC105374654	XR_925791.3 linkuse as main transcript	n.536-2415_536-2412dup		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNND2	ENST00000304623.13 linkuse as main transcript	c.3417+5_3417+6insTAAA		splice_donor_region_variant, intron_variant		1	NM_001332.4	P1	Q9UQB3-1

Frequencies

GnomAD3 genomes

AF:

0.0166

AC:

2519

AN:

152138

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00386

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0124

Gnomad ASJ

AF:

0.00692

Gnomad EAS

AF:

0.00598

Gnomad SAS

AF:

0.0164

Gnomad FIN

AF:

0.0623

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0197

Gnomad OTH

AF:

0.0148

GnomAD3 exomes

AF:

0.0179

AC:

4475

AN:

250228

Hom.:

AF XY:

0.0173

AC XY:

2344

AN XY:

135174

show subpopulations

Gnomad AFR exome

AF:

0.00382

Gnomad AMR exome

AF:

0.00848

Gnomad ASJ exome

AF:

0.00707

Gnomad EAS exome

AF:

0.00774

Gnomad SAS exome

AF:

0.0141

Gnomad FIN exome

AF:

0.0604

Gnomad NFE exome

AF:

0.0180

Gnomad OTH exome

AF:

0.0216

GnomAD4 exome

AF:

0.0201

AC:

29299

AN:

1457548

Hom.:

396

Cov.:

AF XY:

0.0196

AC XY:

14190

AN XY:

725198

show subpopulations

Gnomad4 AFR exome

AF:

0.00222

Gnomad4 AMR exome

AF:

0.00889

Gnomad4 ASJ exome

AF:

0.00651

Gnomad4 EAS exome

AF:

0.00862

Gnomad4 SAS exome

AF:

0.0140

Gnomad4 FIN exome

AF:

0.0637

Gnomad4 NFE exome

AF:

0.0204

Gnomad4 OTH exome

AF:

0.0185

GnomAD4 genome

AF:

0.0166

AC:

2526

AN:

152256

Hom.:

Cov.:

AF XY:

0.0184

AC XY:

1367

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.00385

Gnomad4 AMR

AF:

0.0124

Gnomad4 ASJ

AF:

0.00692

Gnomad4 EAS

AF:

0.00599

Gnomad4 SAS

AF:

0.0164

Gnomad4 FIN

AF:

0.0623

Gnomad4 NFE

AF:

0.0197

Gnomad4 OTH

AF:

0.0189

Alfa

AF:

0.0150

Hom.:

Asia WGS

AF:

0.0190

AC:

AN:

3478

EpiCase

AF:

0.0163

EpiControl

AF:

0.0172

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 28, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over