Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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  • No ClinVar Id was directly found from the curated document
  • ClinVar Id was derived from the Allele Registry.

Variant: NM_001317186.2:c.-684C>T

CA169895

142968 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 2595caa2-c7dd-44bd-ad69-2b5435bd9f8c
Approved on: 2023-08-03
Published on: 2023-08-03

HGVS expressions

NM_001317186.2:c.-684C>T
NC_000016.10:g.68812262C>T
CM000678.2:g.68812262C>T
NC_000016.9:g.68846165C>T
CM000678.1:g.68846165C>T
NC_000016.8:g.67403666C>T
NG_008021.1:g.79971C>T
ENST00000261769.10:c.1136C>T
ENST00000261769.9:c.1136C>T
ENST00000422392.6:c.1136C>T
ENST00000562836.5:n.1207C>T
ENST00000565810.1:n.180C>T
ENST00000566510.5:c.980C>T
ENST00000566612.5:c.1136C>T
ENST00000611625.4:c.1136C>T
ENST00000612417.4:c.1136C>T
ENST00000621016.4:c.1136C>T
NM_004360.3:c.1136C>T
NM_001317184.1:c.1136C>T
NM_001317185.1:c.-480C>T
NM_001317186.1:c.-684C>T
NM_004360.4:c.1136C>T
NM_004360.5:c.1136C>T
NM_001317184.2:c.1136C>T
NM_001317185.2:c.-480C>T
NM_004360.5(CDH1):c.1136C>T (p.Thr379Met)

Likely Benign

Met criteria codes 1
BS2
Not Met criteria codes 8
BS4 BS1 BP2 BP5 PS4 BA1 PP1 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.1136C>T (p.Thr379Met) variant results in a conservative missense change in the Cadherin 3 domain of CDH1. This variant was observed in 2 of 152,226 alleles in the gnomAD population database. However, this variants has also been observed in more than 10 individuals without GC, DGC, gastric SRC tumours or LBC and whose families do not suggest HDGC (BS2). In summary, this variant meets criteria to be classified as Likely Benign based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel: BS2. (CDH1 VCEP specifications version 3.1; 05/22/2023)
Met criteria codes
BS2
This variant has been seen in more than 110 individuals without GC, DGC, gastric SRC tumours, and LBC and whose families do not suggest HDGC. This variant was also identified in a proband with family history of unspecified gastric cancer.
Not Met criteria codes
BS4
To our knowledge, this variant has not been shown to segregate with disease in a family with HDGC.
BS1
This variant occurs at a frequency of 1.3x10-5% (2 in 152,226 alleles) in gnomAD v3.12.
BP2
To our knowledge, this variant has not been reported in the homozygous state.
BP5
To our knowledge, this variant has not been identified in a family with HDGC and alternate molecular basis for disease.
PS4
This variant has been seen in more than 110 individuals without GC, DGC, gastric SRC tumours, and LBC and whose families do not suggest HDGC. This variant was also identified in a proband with family history of unspecified gastric cancer.
BA1
This variant occurs at a frequency of 1.3x10-5% (2 in 152,226 alleles) in gnomAD v3.12.
PP1
To our knowledge, this variant has not been shown to segregate with disease in a family with HDGC.
PP3
In silico predictors do not suggest that this variant alters splicing. Protein-based predictors for missense variants are not applicable for CDH1.
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