Variant 5-10973615-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001332.4(CTNND2):c.3516C>T(p.Phe1172=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0903 in 1,613,890 control chromosomes in the GnomAD database, including 7,097 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 892 hom., cov: 33)

Exomes 𝑓: 0.089 ( 6205 hom. )

Consequence

CTNND2
NM_001332.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.396

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP6

Variant 5-10973615-G-A is Benign according to our data. Variant chr5-10973615-G-A is described in ClinVar as [Benign]. Clinvar id is 1250893.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.396 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNND2	NM_001332.4 linkuse as main transcript	c.3516C>T	p.Phe1172=	synonymous_variant	22/22	ENST00000304623.13
LOC105374654	XR_925791.3 linkuse as main transcript	n.535+3508G>A		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.3516C>T	p.Phe1172=	synonymous_variant	22/22	1	NM_001332.4	P1	Q9UQB3-1

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15555

AN:

152058

Hom.:

889

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.114

Gnomad AMR

AF:

0.0755

Gnomad ASJ

AF:

0.0836

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.0733

Gnomad FIN

AF:

0.0837

Gnomad MID

AF:

0.0637

Gnomad NFE

AF:

0.0839

Gnomad OTH

AF:

0.0927

GnomAD3 exomes

AF:

0.0993

AC:

24841

AN:

250068

Hom.:

1446

AF XY:

0.0971

AC XY:

13138

AN XY:

135286

show subpopulations

Gnomad AFR exome

AF:

0.141

Gnomad AMR exome

AF:

0.0906

Gnomad ASJ exome

AF:

0.0872

Gnomad EAS exome

AF:

0.220

Gnomad SAS exome

AF:

0.0771

Gnomad FIN exome

AF:

0.0814

Gnomad NFE exome

AF:

0.0875

Gnomad OTH exome

AF:

0.0874

GnomAD4 exome

AF:

0.0890

AC:

130164

AN:

1461714

Hom.:

6205

Cov.:

AF XY:

0.0879

AC XY:

63949

AN XY:

727158

show subpopulations

Gnomad4 AFR exome

AF:

0.139

Gnomad4 AMR exome

AF:

0.0884

Gnomad4 ASJ exome

AF:

0.0840

Gnomad4 EAS exome

AF:

0.165

Gnomad4 SAS exome

AF:

0.0772

Gnomad4 FIN exome

AF:

0.0803

Gnomad4 NFE exome

AF:

0.0861

Gnomad4 OTH exome

AF:

0.0959

GnomAD4 genome

AF:

0.102

AC:

15568

AN:

152176

Hom.:

892

Cov.:

AF XY:

0.101

AC XY:

7495

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.139

Gnomad4 AMR

AF:

0.0761

Gnomad4 ASJ

AF:

0.0836

Gnomad4 EAS

AF:

0.207

Gnomad4 SAS

AF:

0.0727

Gnomad4 FIN

AF:

0.0837

Gnomad4 NFE

AF:

0.0839

Gnomad4 OTH

AF:

0.0913

Alfa

AF:

0.0832

Hom.:

1131

Bravo

AF:

0.106

Asia WGS

AF:

0.106

AC:

368

AN:

3478

EpiCase

AF:

0.0805

EpiControl

AF:

0.0775

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

Jul 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

Cadd

Benign

7.0

Dann

Benign

0.70

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