16-68833484-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP2BA1

This summary comes from the ClinGen Evidence Repository: The NM_004360.5(CDH1):c.2634C>T (p.Gly878=) variant has an allele frequency of 0.03601 (3.6%, 899/24962 alleles, 20 homozygotes) in the African 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. LINK:https://erepo.genome.network/evrepo/ui/classification/CA168961/MONDO:0007648/007

Frequency

Genomes: š‘“ 0.016 ( 37 hom., cov: 32)
Exomes š‘“: 0.0075 ( 139 hom. )

Consequence

CDH1
NM_004360.5 synonymous

Scores

2

Clinical Significance

Benign reviewed by expert panel B:19

Conservation

PhyloP100: -4.03
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP2
For more information check the summary or visit ClinGen Evidence Repository.
BA1
For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDH1NM_004360.5 linkc.2634C>T p.Gly878Gly synonymous_variant 16/16 ENST00000261769.10 NP_004351.1 P12830-1A0A0U2ZQU7B3GN61
CDH1NM_001317184.2 linkc.2451C>T p.Gly817Gly synonymous_variant 15/15 NP_001304113.1 P12830-2B3GN61
CDH1NM_001317185.2 linkc.1086C>T p.Gly362Gly synonymous_variant 16/16 NP_001304114.1 P12830B3GN61Q9UII7
CDH1NM_001317186.2 linkc.669C>T p.Gly223Gly synonymous_variant 15/15 NP_001304115.1 P12830B3GN61

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDH1ENST00000261769.10 linkc.2634C>T p.Gly878Gly synonymous_variant 16/161 NM_004360.5 ENSP00000261769.4 P12830-1

Frequencies

GnomAD3 genomes
AF:
0.0159
AC:
2422
AN:
152036
Hom.:
37
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0356
Gnomad AMI
AF:
0.0385
Gnomad AMR
AF:
0.0159
Gnomad ASJ
AF:
0.0112
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00269
Gnomad FIN
AF:
0.00595
Gnomad MID
AF:
0.123
Gnomad NFE
AF:
0.00690
Gnomad OTH
AF:
0.0234
GnomAD3 exomes
AF:
0.00919
AC:
2311
AN:
251410
Hom.:
42
AF XY:
0.00850
AC XY:
1155
AN XY:
135878
show subpopulations
Gnomad AFR exome
AF:
0.0372
Gnomad AMR exome
AF:
0.0129
Gnomad ASJ exome
AF:
0.0106
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00242
Gnomad FIN exome
AF:
0.00513
Gnomad NFE exome
AF:
0.00743
Gnomad OTH exome
AF:
0.0199
GnomAD4 exome
AF:
0.00751
AC:
10977
AN:
1461474
Hom.:
139
Cov.:
32
AF XY:
0.00741
AC XY:
5385
AN XY:
727038
show subpopulations
Gnomad4 AFR exome
AF:
0.0384
Gnomad4 AMR exome
AF:
0.0140
Gnomad4 ASJ exome
AF:
0.00968
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.00230
Gnomad4 FIN exome
AF:
0.00498
Gnomad4 NFE exome
AF:
0.00635
Gnomad4 OTH exome
AF:
0.0127
GnomAD4 genome
AF:
0.0159
AC:
2424
AN:
152154
Hom.:
37
Cov.:
32
AF XY:
0.0156
AC XY:
1159
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.0356
Gnomad4 AMR
AF:
0.0159
Gnomad4 ASJ
AF:
0.0112
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00269
Gnomad4 FIN
AF:
0.00595
Gnomad4 NFE
AF:
0.00690
Gnomad4 OTH
AF:
0.0232
Alfa
AF:
0.0107
Hom.:
16
Bravo
AF:
0.0181
Asia WGS
AF:
0.00779
AC:
27
AN:
3478
EpiCase
AF:
0.0107
EpiControl
AF:
0.0110

ClinVar

Significance: Benign
Submissions summary: Benign:19
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

not specified Benign:6
Likely benign, no assertion criteria providedclinical testingMayo Clinic Laboratories, Mayo Clinic-- -
Benign, no assertion criteria providedclinical testingJoint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+-- -
Benign, criteria provided, single submitterclinical testingCenter for Genomic Medicine, Rigshospitalet, Copenhagen University HospitalAug 15, 2023- -
Benign, no assertion criteria providedclinical testingGenome Diagnostics Laboratory, Amsterdam University Medical Center-- -
Benign, no assertion criteria providedclinical testingClinical Genetics, Academic Medical Center-- -
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesApr 11, 2016- -
Hereditary diffuse gastric adenocarcinoma Benign:4
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This 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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -
Benign, criteria provided, single submitterclinical testingMyriad Genetics, Inc.Sep 24, 2024This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing. -
Benign, criteria provided, single submitterclinical testingEuropean Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de InvestigaĆ§Ć£o e InovaĆ§Ć£o em SaĆŗde, University of PortoAug 01, 2022BA1; BP2_Strong (PMID: 30311375) -
not provided Benign:3
Benign, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesNov 29, 2023- -
Benign, criteria provided, single submitterclinical testingGeneDxMar 03, 2015- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Hereditary cancer-predisposing syndrome Benign:3
Benign, criteria provided, single submitterclinical testingAmbry GeneticsNov 18, 2014This 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. -
Benign, criteria provided, single submitterclinical testingColor Diagnostics, LLC DBA Color HealthApr 02, 2015- -
Likely benign, no assertion criteria providedclinical testingTrue Health DiagnosticsDec 01, 2017- -
Malignant tumor of breast Benign:1
Benign, no assertion criteria providedclinical testingDepartment of Pathology and Laboratory Medicine, Sinai Health System-The CDH1 p.Gly878= variant was identified in 7 of 438 proband chromosomes (frequency: 0.02) from individuals or families with hereditary diffuse gastric cancer (Jakubowska 2010, Oliveira 2002, Guindalini 2019, El-Husny 2014). The variant was also identified in dbSNP (ID: rs2229044) as "With other allele" and ClinVar (classified as benign by Invitae, Ambry Genetics and two other submitters; and as likely benign by three submitters). The variant was identified in control databases in 2637 of 277164 chromosomes (47 homozygous) at a frequency of 0.009, increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 851 of 24030 chromosomes (freq: 0.04), Other in 122 of 6468 chromosomes (freq: 0.02), Latino in 430 of 34420 chromosomes (freq: 0.01), European in 911 of 126668 chromosomes (freq: 0.007), Ashkenazi Jewish in 112 of 10152 chromosomes (freq: 0.01), East Asian in 1 of 18864 chromosomes (freq: 0.00005), Finnish in 137 of 25780 chromosomes (freq: 0.005), and South Asian in 73 of 30782 chromosomes (freq: 0.002). The p.Gly878= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information, this variant meets our laboratory's criteria to be classified as benign. -
CDH1-related diffuse gastric and lobular breast cancer syndrome Benign:1
Benign, reviewed by expert panelcurationClinGen CDH1 Variant Curation Expert PanelAug 10, 2023The NM_004360.5(CDH1):c.2634C>T (p.Gly878=) variant has an allele frequency of 0.03601 (3.6%, 899/24962 alleles, 20 homozygotes) in the African 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. -
Malignant tumor of prostate Benign:1
Benign, criteria provided, single submitterclinical testingKCCC/NGS Laboratory, Kuwait Cancer Control CenterJul 07, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
5.6
DANN
Benign
0.76

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.

Other links and lift over

dbSNP: rs2229044; hg19: chr16-68867387; COSMIC: COSV55731553; API