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
Consequence
NM_004360.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH1 | NM_004360.5 | c.2634C>T | p.Gly878Gly | synonymous_variant | 16/16 | ENST00000261769.10 | NP_004351.1 | |
CDH1 | NM_001317184.2 | c.2451C>T | p.Gly817Gly | synonymous_variant | 15/15 | NP_001304113.1 | ||
CDH1 | NM_001317185.2 | c.1086C>T | p.Gly362Gly | synonymous_variant | 16/16 | NP_001304114.1 | ||
CDH1 | NM_001317186.2 | c.669C>T | p.Gly223Gly | synonymous_variant | 15/15 | NP_001304115.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0159 AC: 2422AN: 152036Hom.: 37 Cov.: 32
GnomAD3 exomes AF: 0.00919 AC: 2311AN: 251410Hom.: 42 AF XY: 0.00850 AC XY: 1155AN XY: 135878
GnomAD4 exome AF: 0.00751 AC: 10977AN: 1461474Hom.: 139 Cov.: 32 AF XY: 0.00741 AC XY: 5385AN XY: 727038
GnomAD4 genome AF: 0.0159 AC: 2424AN: 152154Hom.: 37 Cov.: 32 AF XY: 0.0156 AC XY: 1159AN XY: 74388
ClinVar
Submissions by phenotype
not specified Benign:6
Likely benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 11, 2016 | - - |
Hereditary diffuse gastric adenocarcinoma Benign:4
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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 | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Sep 24, 2024 | This 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 submitter | clinical testing | European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de InvestigaĆ§Ć£o e InovaĆ§Ć£o em SaĆŗde, University of Porto | Aug 01, 2022 | BA1; BP2_Strong (PMID: 30311375) - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Hereditary cancer-predisposing syndrome Benign:3
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. - |
Benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Apr 02, 2015 | - - |
Likely benign, no assertion criteria provided | clinical testing | True Health Diagnostics | Dec 01, 2017 | - - |
Malignant tumor of breast Benign:1
Benign, no assertion criteria provided | clinical testing | Department 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 panel | curation | ClinGen CDH1 Variant Curation Expert Panel | Aug 10, 2023 | 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. - |
Malignant tumor of prostate Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at