Variant 5-10973815-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001332.4(CTNND2):c.3418-102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,323,536 control chromosomes in the GnomAD database, including 46,438 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.30 ( 7319 hom., cov: 32)

Exomes 𝑓: 0.25 ( 39119 hom. )

Consequence

CTNND2
NM_001332.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.71

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BP6

Variant 5-10973815-T-C is Benign according to our data. Variant chr5-10973815-T-C is described in ClinVar as [Benign]. Clinvar id is 1287782.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 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.3418-102A>G		intron_variant		ENST00000304623.13
LOC105374654	XR_925791.3 linkuse as main transcript	n.535+3708T>C		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.3418-102A>G		intron_variant		1	NM_001332.4	P1	Q9UQB3-1

Frequencies

GnomAD3 genomes

AF:

0.296

AC:

44927

AN:

151972

Hom.:

7290

Cov.:

show subpopulations

Gnomad AFR

AF:

0.433

Gnomad AMI

AF:

0.252

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.311

Gnomad EAS

AF:

0.218

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.283

GnomAD4 exome

AF:

0.253

AC:

296916

AN:

1171446

Hom.:

39119

AF XY:

0.250

AC XY:

144318

AN XY:

577368

show subpopulations

Gnomad4 AFR exome

AF:

0.451

Gnomad4 AMR exome

AF:

0.205

Gnomad4 ASJ exome

AF:

0.310

Gnomad4 EAS exome

AF:

0.172

Gnomad4 SAS exome

AF:

0.133

Gnomad4 FIN exome

AF:

0.281

Gnomad4 NFE exome

AF:

0.258

Gnomad4 OTH exome

AF:

0.260

GnomAD4 genome

AF:

0.296

AC:

45009

AN:

152090

Hom.:

7319

Cov.:

AF XY:

0.293

AC XY:

21755

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.434

Gnomad4 AMR

AF:

0.226

Gnomad4 ASJ

AF:

0.311

Gnomad4 EAS

AF:

0.218

Gnomad4 SAS

AF:

0.128

Gnomad4 FIN

AF:

0.276

Gnomad4 NFE

AF:

0.249

Gnomad4 OTH

AF:

0.285

Alfa

AF:

0.257

Hom.:

4890

Bravo

AF:

0.304

Asia WGS

AF:

0.192

AC:

670

AN:

3478

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

-1.0

CADD

Benign

0.18

DANN

Benign

0.41

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