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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Variant: NM_004360.5(CDH1):c.1948_1949del (p.Ile650fs)

CA658658495

483276 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: b4d1c92f-eadb-414e-a15c-627f87dcbebf
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.5:c.1948_1949del
NM_004360.5(CDH1):c.1948_1949del (p.Ile650fs)
NC_000016.10:g.68823410_68823411del
CM000678.2:g.68823410_68823411del
NC_000016.9:g.68857313_68857314del
CM000678.1:g.68857313_68857314del
NC_000016.8:g.67414814_67414815del
NG_008021.1:g.91119_91120del
ENST00000261769.10:c.1948_1949del
ENST00000261769.9:c.1948_1949del
ENST00000422392.6:c.1765_1766del
ENST00000562118.1:n.166_167del
ENST00000562836.5:n.2019_2020del
ENST00000566510.5:c.*614_*615del
ENST00000566612.5:c.*188_*189del
ENST00000611625.4:c.2011_2012del
ENST00000612417.4:c.1830+1291_1830+1292del
ENST00000621016.4:c.1865+1256_1865+1257del
NM_004360.3:c.1948_1949del
NM_001317184.1:c.1765_1766del
NM_001317185.1:c.400_401del
NM_001317186.1:c.-18_-17del
NM_004360.4:c.1948_1949del
NM_001317184.2:c.1765_1766del
NM_001317185.2:c.400_401del
NM_001317186.2:c.-18_-17del

Pathogenic

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

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.1948_1949del p.(Ile650fs) 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
PVS1
Exon 13 of 16, predicted NMD.
PM5_Supporting
Exon 13 of 16, predicted NMD.
PM2_Supporting
Absent in population databases.
Not Met criteria codes
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
BS1
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
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
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
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
SCV000669079.2 (Ambry) - proband LBC in 40s, father stomach (no pathology). Not in published studies.
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
PP1
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
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
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
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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