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_004360.5(CDH1):c.1917_1918del (p.Ile640fs)

CA658798631

532477 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: b95580d2-6d28-4fd0-a8b8-b862f75d6cc8
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.5:c.1917_1918del
NM_004360.5(CDH1):c.1917_1918del (p.Ile640fs)
NC_000016.10:g.68822206_68822207del
CM000678.2:g.68822206_68822207del
NC_000016.9:g.68856109_68856110del
CM000678.1:g.68856109_68856110del
NC_000016.8:g.67413610_67413611del
NG_008021.1:g.89915_89916del
ENST00000261769.10:c.1917_1918del
ENST00000261769.9:c.1917_1918del
ENST00000422392.6:c.1734_1735del
ENST00000562836.5:n.1988_1989del
ENST00000566510.5:c.*583_*584del
ENST00000566612.5:c.*157_*158del
ENST00000611625.4:c.1980_1981del
ENST00000612417.4:c.1830+87_1830+88del
ENST00000621016.4:c.1865+52_1865+53del
NM_004360.3:c.1917_1918del
NM_001317184.1:c.1734_1735del
NM_001317185.1:c.369_370del
NM_001317186.1:c.-49_-48del
NM_004360.4:c.1917_1918del
NM_001317184.2:c.1734_1735del
NM_001317185.2:c.369_370del
NM_001317186.2:c.-49_-48del
More

Pathogenic

Met criteria codes 3
PM2_Supporting PVS1 PM5_Supporting
Not Met criteria codes 23
BP3 BP4 BP1 BP2 BP7 BP5 PS1 PS3 PS2 PS4 PM4 PM1 PM3 BA1 PM6 PP3 PP2 PP4 PP1 BS2 BS3 BS4 BS1

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.1917_1918del p.(Ile640fs) variant is predicted to result in a premature stop codon that leads to nonsense mediate decay (PVS1 and PM5_supporting). The variant is absent in the gnomAD cohort (PM2_supporting; http://gnomad.broadinstitute.org). Therefore, this variant meets criteria to be classified as pathogenic based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (CDH1 VCEP specifications version 3.1): PVS1, PM2_supporting, PM5_supporting.
Met criteria codes
PM2_Supporting
Absent in population databases.
PVS1
Exon 12 of 16, predicted NMD.
PM5_Supporting
Exon 12 of 16, predicted NMD.
Not Met criteria codes
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
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
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
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
PS1
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
SCV000760850.2 (Invitae) - one family, does not meet HDGC criteria (no pathology). Not in published studies.
PM4
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
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
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
PP3
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
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
BS2
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
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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