The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_004360.5(CDH1):c.833-9C>G

CA10583413

239915 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
UUID: 7e1429df-b9e4-4ba3-810e-c19d3cc64d4d
Approved on: 2023-08-28
Published on: 2023-09-27

HGVS expressions

NM_004360.5:c.833-9C>G
NM_004360.5(CDH1):c.833-9C>G
NC_000016.10:g.68811675C>G
CM000678.2:g.68811675C>G
NC_000016.9:g.68845578C>G
CM000678.1:g.68845578C>G
NC_000016.8:g.67403079C>G
NG_008021.1:g.79384C>G
ENST00000261769.10:c.833-9C>G
ENST00000261769.9:c.833-9C>G
ENST00000422392.6:c.833-9C>G
ENST00000561751.1:c.455-9C>G
ENST00000562836.5:n.904-9C>G
ENST00000566510.5:c.677-9C>G
ENST00000566612.5:c.833-9C>G
ENST00000611625.4:c.833-9C>G
ENST00000612417.4:c.833-9C>G
ENST00000621016.4:c.833-9C>G
NM_004360.3:c.833-9C>G
NM_001317184.1:c.833-9C>G
NM_001317185.1:c.-783-9C>G
NM_001317186.1:c.-987-9C>G
NM_004360.4:c.833-9C>G
NM_001317184.2:c.833-9C>G
NM_001317185.2:c.-783-9C>G
NM_001317186.2:c.-987-9C>G

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP3 PS4_Moderate PS3
Not Met criteria codes 14
PP4 PP2 BA1 PM3 PM1 BS3 BS1 BS2 PVS1 PS1 BP7 BP3 BP4 BP1

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 NM_004360.5(CDH1):c.833-9C>G variant is an intronic variant in the vicinity of the 3' splice site of intron 6. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). There are at least 3 in silico predictors in agreement that this variant affects splicing (PP3). Additionally, this variant has been reported in at least two families meeting HDGC clinical criteria (PS4_Moderate; internal laboratory contributor). Furthermore, RNA analysis has demonstrated a novel eight base pair insertion (TCTTCCAG) resulting in a premature stop codon (p.G278Vfs*7) (PS3, internal data). In summary, this variant is classified as likely pathogenic based on ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): PS3, PS4_supporting, PM2_supporting, PP3.
Met criteria codes
PM2_Supporting
The NM_004360.5(CDH1):c.833-9C>G is not present in population databases.
PP3
The results from three in silico predictors, SpliceAI, MaxEntScan and NetGene2, predict a damaging effect on CDH1 function (PP3).
PS4_Moderate
Two families meet HDGC criteria (Ambry, Invitae).
PS3
RNA studies showed r.832_833ins833-8_833-1 p.G278Vfs*7 associated with this variant (Ambry).
Not Met criteria codes
PP4
Not applicable for CDH1.
PP2
Not applicable for CDH1.
BA1
The NM_004360.5(CDH1):c.833-9C>G is not present in population databases.
PM3
Not applicable for CDH1.
PM1
Not applicable for CDH1.
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
The NM_004360.5(CDH1):c.833-9C>G is not present in population databases.
BS2
One family does not meet HDGC criteria.
PVS1
Th NM_004360.5(CDH1):c.833-9C>G variant is an intronic variant.
PS1
Not applicable for CDH1.
BP7
The NM_004360.5(CDH1):c.833-9C>G variant is an intronic variant.
BP3
Not applicable for CDH1.
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
Not applicable for CDH1.
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