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]

Variant: NM_004360.4(CDH1):c.1138-3C>T

CA188674

184346 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 44ff0837-63d3-46af-9fc3-d319e5146005
Approved on: 2023-08-24
Published on: 2023-08-24

HGVS expressions

NM_004360.4:c.1138-3C>T
NM_004360.4(CDH1):c.1138-3C>T
NC_000016.10:g.68813310C>T
CM000678.2:g.68813310C>T
NC_000016.9:g.68847213C>T
CM000678.1:g.68847213C>T
NC_000016.8:g.67404714C>T
NG_008021.1:g.81019C>T
ENST00000261769.10:c.1138-3C>T
ENST00000261769.9:c.1138-3C>T
ENST00000422392.6:c.1137+1047C>T
ENST00000562836.5:n.1209-3C>T
ENST00000565810.1:n.182-3C>T
ENST00000566510.5:c.982-3C>T
ENST00000566612.5:c.1138-3C>T
ENST00000611625.4:c.1138-3C>T
ENST00000612417.4:c.1138-3C>T
ENST00000621016.4:c.1138-3C>T
NM_004360.3:c.1138-3C>T
NM_001317184.1:c.1137+1047C>T
NM_001317185.1:c.-478-3C>T
NM_001317186.1:c.-682-3C>T
NM_004360.5:c.1138-3C>T
NM_001317184.2:c.1137+1047C>T
NM_001317185.2:c.-478-3C>T
NM_001317186.2:c.-682-3C>T
NM_004360.5(CDH1):c.1138-3C>T
More

Likely Benign

Met criteria codes 2
BS1 BP4
Not Met criteria codes 24
PS2 PS4 PS3 PS1 PP4 PP1 PP2 PP3 PM3 PM1 PM4 PM5 PM6 PM2 BA1 BS2 BS4 BS3 BP2 BP3 BP1 PVS1 BP5 BP7

Evidence Links 1

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.1138-3C>T variant has an allele frequency of 0.00121 (0.121%, 29/24,036 alleles) in the African subpopulation of the gnomAD cohort (BS1). There are at least 3 in silico predictors in agreement that this variant does not affect splicing (BP4). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel: BS1, BP4 (Variant Interpretation Guidelines Version 3.1).
Met criteria codes
BS1
0.15% in AA subpopulation with 16 alleles (exceeds cutoff of 0.1%).
Japanese incidence of stomach cancer is 0.07%. PubMed:15322508
BP4
Alteration not predicted to impact splicing in HSF, MaxEntScan, or NNSPLICE
Not Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
Alteration not predicted to impact splicing in HSF, MaxEntScan, or NNSPLICE
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
0.15% in AA subpopulation with 16 alleles (exceeds cutoff of 0.1%).
BA1
0.15% in AA subpopulation with 16 alleles (exceeds cutoff of 0.1%).
BS2
48 confirmed hets - need to confirm if hets are unaffected.
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
Alteration not predicted to impact splicing in HSF, MaxEntScan, or NNSPLICE
Curation History
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