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Variant: NM_004360.5(CDH1):c.2450C>T (p.Ala817Val)

CA166465

141802 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
UUID: 9d7dbe5b-ee8e-4a22-8ebe-0cdae8f8b7b0

HGVS expressions

NM_004360.5:c.2450C>T
NM_004360.5(CDH1):c.2450C>T (p.Ala817Val)
NC_000016.10:g.68833300C>T
CM000678.2:g.68833300C>T
NC_000016.9:g.68867203C>T
CM000678.1:g.68867203C>T
NC_000016.8:g.67424704C>T
NG_008021.1:g.101009C>T
ENST00000261769.10:c.2450C>T
ENST00000261769.9:c.2450C>T
ENST00000422392.6:c.2267C>T
ENST00000562118.1:n.668C>T
ENST00000562836.5:n.2521C>T
ENST00000566510.5:c.*1116C>T
ENST00000566612.5:c.*690C>T
ENST00000611625.4:c.2513C>T
ENST00000612417.4:c.1854-891C>T
ENST00000621016.4:c.1866-903C>T
NM_004360.3:c.2450C>T
NM_001317184.1:c.2267C>T
NM_001317185.1:c.902C>T
NM_001317186.1:c.485C>T
NM_004360.4:c.2450C>T
NM_001317184.2:c.2267C>T
NM_001317185.2:c.902C>T
NM_001317186.2:c.485C>T

Likely Benign

Met criteria codes 1
BS2
Not Met criteria codes 5
PM2 BS1 PS4 BA1 PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen CDH1 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 3.1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
CDH1 VCEP
The c.2450C>T (p.Ala817Val) variant results in a missense change in the last exon of CDH1. This variant is present at a frequency 3.3x10-5 (5 of 152,172 alleles) in the gnomAD population database v3.1.2. This variant has been observed in 104 individuals without DGC, LBC or SRC tumours and whose families do not suggest HDGC (BS2; internal laboratory contributors). In vitro studies of the A817V variant suggest reduced binding of B-catenin and reduced cell aggregation in a HEK293T cell model (PMID: 33929593). However, evaluation of the use of functional data by the VCEP indicates that functional data currently available for missense variants cannot yet predict the pathogenicity of CDH1 variants, and it is therefore not considered in the classification for any CDH1 missense variant (Lee et al, 2018; PMID: 30311375). As such, published information from in vitro or in vivo assays assessing impact on function for this missense variant has not been considered for variant curation. In summary, this variant is classified as likely benign based on ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel: BS2.
Met criteria codes
BS2
This variant has been identified in more than 104 individuals with DGC, LBC or SRC tumours and whose families do not suggest HDGC. This variant was reported in a family with multiple gliomas and without gastric or lobular breast cancer (PMID: 33929593).
Not Met criteria codes
PM2
This variant is present at a frequency of 0.00002 (6 of 251,458 alleles) in gnomAD.
BS1
This variant is present at a frequency of 0.00002 (6 of 251,458 alleles) in gnomAD.
PS4
This variant has been identified in more than 104 individuals with DGC, LBC or SRC tumours and whose families do not suggest HDGC. This variant was reported in a family with multiple gliomas and without gastric or lobular breast cancer (PMID: 33929593).
BA1
This variant is present at a frequency of 0.00002 (6 of 251,458 alleles) in gnomAD.
PP3
This variant is not predicted to impact splicing.
Approved on: 2023-09-25
Published on: 2023-09-27
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