Variant rs17183619 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001332.4(CTNND2):c.2278-98A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0951 in 1,304,248 control chromosomes in the GnomAD database, including 6,434 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.077 ( 591 hom., cov: 32)

Exomes 𝑓: 0.097 ( 5843 hom. )

Consequence

CTNND2
NM_001332.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0110

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 5-11111141-T-G is Benign according to our data. Variant chr5-11111141-T-G is described in ClinVar as [Benign]. Clinvar id is 1228070.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNND2	NM_001332.4 linkuse as main transcript	c.2278-98A>C		intron_variant		ENST00000304623.13	NP_001323.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTNND2	ENST00000304623.13 linkuse as main transcript	c.2278-98A>C		intron_variant		1	NM_001332.4	ENSP00000307134	P1	Q9UQB3-1

Frequencies

GnomAD3 genomes

AF:

0.0773

AC:

11757

AN:

152130

Hom.:

587

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0195

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.0671

Gnomad ASJ

AF:

0.0694

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.0829

GnomAD4 exome

AF:

0.0974

AC:

112236

AN:

1152000

Hom.:

5843

AF XY:

0.0978

AC XY:

55741

AN XY:

570080

show subpopulations

Gnomad4 AFR exome

AF:

0.0149

Gnomad4 AMR exome

AF:

0.0521

Gnomad4 ASJ exome

AF:

0.0712

Gnomad4 EAS exome

AF:

0.122

Gnomad4 SAS exome

AF:

0.112

Gnomad4 FIN exome

AF:

0.127

Gnomad4 NFE exome

AF:

0.0987

Gnomad4 OTH exome

AF:

0.0932

GnomAD4 genome

AF:

0.0773

AC:

11770

AN:

152248

Hom.:

591

Cov.:

AF XY:

0.0784

AC XY:

5836

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.0194

Gnomad4 AMR

AF:

0.0672

Gnomad4 ASJ

AF:

0.0694

Gnomad4 EAS

AF:

0.110

Gnomad4 SAS

AF:

0.117

Gnomad4 FIN

AF:

0.127

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.0872

Alfa

AF:

0.0817

Hom.:

Bravo

AF:

0.0707

Asia WGS

AF:

0.0930

AC:

324

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.38

DANN

Benign

0.69

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

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