rs2276330

Variant summary

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

The NM_004360.5(CDH1):c.1937-13T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,582,056 control chromosomes in the GnomAD database, including 12,547 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

Frequency

Genomes: 𝑓 0.095 ( 871 hom., cov: 31)

Exomes 𝑓: 0.12 ( 11676 hom. )

Consequence

CDH1
NM_004360.5 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign reviewed by expert panel U:1B:12

Conservation

PhyloP100: 0.184

Variant links:

Genes affected

CDH1 (HGNC:1748): (cadherin 1) 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. Mutations in this gene are correlated with gastric, breast, colorectal, thyroid and ovarian cancer. Loss of function of this gene is thought to contribute to cancer progression by increasing proliferation, invasion, and/or metastasis. The ectodomain of this protein mediates bacterial adhesion to mammalian cells and the cytoplasmic domain is required for internalization. This gene is present in a gene cluster with other members of the cadherin family on chromosome 16. [provided by RefSeq, Nov 2015]

CDH1 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 16-68823386-T-C is Benign according to our data. Variant chr16-68823386-T-C is described in ClinVar as [Benign]. Clinvar id is 140806.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr16-68823386-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CDH1	NM_004360.5 linkuse as main transcript	c.1937-13T>C	splice_polypyrimidine_tract_variant, intron_variant	ENST00000261769.10
CDH1	NM_001317184.2 linkuse as main transcript	c.1754-13T>C	splice_polypyrimidine_tract_variant, intron_variant
CDH1	NM_001317185.2 linkuse as main transcript	c.389-13T>C	splice_polypyrimidine_tract_variant, intron_variant
CDH1	NM_001317186.2 linkuse as main transcript	c.-29-13T>C	splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH1	ENST00000261769.10 linkuse as main transcript	c.1937-13T>C		splice_polypyrimidine_tract_variant, intron_variant		1	NM_004360.5	P1	P12830-1
	ENST00000563916.1 linkuse as main transcript	n.141A>G		non_coding_transcript_exon_variant	1/3	4

Frequencies

GnomAD3 genomes

AF:

0.0949

AC:

14433

AN:

152152

Hom.:

872

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0243

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.0666

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.0705

Gnomad SAS

AF:

0.0536

Gnomad FIN

AF:

0.159

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.137

Gnomad OTH

AF:

0.0920

GnomAD3 exomes

AF:

0.103

AC:

25875

AN:

250252

Hom.:

1597

AF XY:

0.105

AC XY:

14188

AN XY:

135466

show subpopulations

Gnomad AFR exome

AF:

0.0211

Gnomad AMR exome

AF:

0.0476

Gnomad ASJ exome

AF:

0.121

Gnomad EAS exome

AF:

0.0795

Gnomad SAS exome

AF:

0.0537

Gnomad FIN exome

AF:

0.165

Gnomad NFE exome

AF:

0.136

Gnomad OTH exome

AF:

0.111

GnomAD4 exome

AF:

0.122

AC:

173911

AN:

1429786

Hom.:

11676

Cov.:

AF XY:

0.120

AC XY:

85559

AN XY:

713624

show subpopulations

Gnomad4 AFR exome

AF:

0.0225

Gnomad4 AMR exome

AF:

0.0497

Gnomad4 ASJ exome

AF:

0.127

Gnomad4 EAS exome

AF:

0.0544

Gnomad4 SAS exome

AF:

0.0543

Gnomad4 FIN exome

AF:

0.169

Gnomad4 NFE exome

AF:

0.133

Gnomad4 OTH exome

AF:

0.116

GnomAD4 genome

AF:

0.0948

AC:

14431

AN:

152270

Hom.:

871

Cov.:

AF XY:

0.0932

AC XY:

6938

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0243

Gnomad4 AMR

AF:

0.0665

Gnomad4 ASJ

AF:

0.132

Gnomad4 EAS

AF:

0.0709

Gnomad4 SAS

AF:

0.0536

Gnomad4 FIN

AF:

0.159

Gnomad4 NFE

AF:

0.137

Gnomad4 OTH

AF:

0.0915

Alfa

AF:

0.122

Hom.:

1841

Bravo

AF:

0.0869

Asia WGS

AF:

0.0500

AC:

174

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Uncertain:1Benign:12

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

not specified

Benign:5

Benign, no assertion criteria provided	clinical testing	Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

not provided

Uncertain:1Benign:1

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	This variant is associated with the following publications: (PMID: 24204729) -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	- -

Hereditary diffuse gastric adenocarcinoma

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	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. -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -

Hereditary cancer-predisposing syndrome

Benign:2

Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 19, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Nov 18, 2014	This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Malignant tumor of prostate

Benign:1

Benign, criteria provided, single submitter

clinical testing

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Jul 07, 2023

- -

CDH1-related diffuse gastric and lobular breast cancer syndrome

Benign:1

Benign, reviewed by expert panel

curation

ClinGen CDH1 Variant Curation Expert Panel

Aug 10, 2023

The NM_004360.5(CDH1):c.1937-13T>C variant has an allele frequency of 0.16607 (16.6%, 4107/24730 alleles, 330 homozygotes) in the European (Finnish) subpopulation of the gnomAD v2.1.1 cohort (BA1; BP2). Therefore, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BA1, BP2. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

Cadd

Benign

9.0

Dann

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

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