rs2296409

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001793.6(CDH3):c.720G>A(p.Thr240Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 1,610,936 control chromosomes in the GnomAD database, including 307,296 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.63 ( 29939 hom., cov: 30)

Exomes 𝑓: 0.61 ( 277357 hom. )

Consequence

CDH3
NM_001793.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -3.96

Variant links:

Genes affected

CDH3 (HGNC:1762): (cadherin 3) This gene encodes a classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium-dependent cell-cell adhesion protein is comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. This gene is located in a gene cluster in a region on the long arm of chromosome 16 that is involved in loss of heterozygosity events in breast and prostate cancer. In addition, aberrant expression of this protein is observed in cervical adenocarcinomas. Mutations in this gene are associated with hypotrichosis with juvenile macular dystrophy and ectodermal dysplasia, ectrodactyly, and macular dystrophy syndrome (EEMS). [provided by RefSeq, Nov 2015]

CDH3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 16-68679827-G-A is Benign according to our data. Variant chr16-68679827-G-A is described in ClinVar as [Benign]. Clinvar id is 320229.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.96 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH3	NM_001793.6 link	c.720G>A	p.Thr240Thr	synonymous_variant	Exon 7 of 16	ENST00000264012.9	NP_001784.2	P22223-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH3	ENST00000264012.9 link	c.720G>A	p.Thr240Thr	synonymous_variant	Exon 7 of 16	1	NM_001793.6	ENSP00000264012.4		P22223-1

Frequencies

GnomAD3 genomes

AF:

0.627

AC:

94977

AN:

151494

Hom.:

29909

Cov.:

show subpopulations

Gnomad AFR

AF:

0.674

Gnomad AMI

AF:

0.719

Gnomad AMR

AF:

0.543

Gnomad ASJ

AF:

0.572

Gnomad EAS

AF:

0.628

Gnomad SAS

AF:

0.546

Gnomad FIN

AF:

0.610

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.627

Gnomad OTH

AF:

0.618

GnomAD3 exomes

AF:

0.589

AC:

148094

AN:

251386

Hom.:

44118

AF XY:

0.590

AC XY:

80223

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.675

Gnomad AMR exome

AF:

0.473

Gnomad ASJ exome

AF:

0.579

Gnomad EAS exome

AF:

0.609

Gnomad SAS exome

AF:

0.543

Gnomad FIN exome

AF:

0.604

Gnomad NFE exome

AF:

0.620

Gnomad OTH exome

AF:

0.590

GnomAD4 exome

AF:

0.615

AC:

897082

AN:

1459324

Hom.:

277357

Cov.:

AF XY:

0.612

AC XY:

444731

AN XY:

726122

show subpopulations

Gnomad4 AFR exome

AF:

0.669

Gnomad4 AMR exome

AF:

0.484

Gnomad4 ASJ exome

AF:

0.580

Gnomad4 EAS exome

AF:

0.633

Gnomad4 SAS exome

AF:

0.542

Gnomad4 FIN exome

AF:

0.612

Gnomad4 NFE exome

AF:

0.625

Gnomad4 OTH exome

AF:

0.612

GnomAD4 genome

AF:

0.627

AC:

95063

AN:

151612

Hom.:

29939

Cov.:

AF XY:

0.622

AC XY:

46080

AN XY:

74064

show subpopulations

Gnomad4 AFR

AF:

0.674

Gnomad4 AMR

AF:

0.543

Gnomad4 ASJ

AF:

0.572

Gnomad4 EAS

AF:

0.627

Gnomad4 SAS

AF:

0.546

Gnomad4 FIN

AF:

0.610

Gnomad4 NFE

AF:

0.627

Gnomad4 OTH

AF:

0.619

Alfa

AF:

0.616

Hom.:

40079

Bravo

AF:

0.624

Asia WGS

AF:

0.554

AC:

1929

AN:

3476

EpiCase

AF:

0.621

EpiControl

AF:

0.618

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Apr 26, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

EEM syndrome

Benign:2

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Congenital hypotrichosis with juvenile macular dystrophy

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

0.28

DANN

Benign

0.43

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