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]
Link to SEPIO compliant JSON-LD document

Variant: NM_004360.4(CDH1):c.1711+2_1711+7delTAAGGG

CA195350

186618 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: b1199911-3a8f-4212-a682-fae7a79aae9b

HGVS expressions

NM_004360.4:c.1711+2_1711+7del
NM_004360.4(CDH1):c.1711+2_1711+7delTAAGGG
NC_000016.10:g.68819427_68819432del
CM000678.2:g.68819427_68819432del
NC_000016.9:g.68853330_68853335del
CM000678.1:g.68853330_68853335del
NC_000016.8:g.67410831_67410836del
NG_008021.1:g.87136_87141del
ENST00000261769.10:c.1711+2_1711+7del
ENST00000261769.9:c.1711+2_1711+7del
ENST00000422392.6:c.1528+2_1528+7del
ENST00000562836.5:n.1782+2_1782+7del
ENST00000566510.5:c.*377+2_*377+7del
ENST00000566612.5:c.1566-2574_1566-2569del
ENST00000611625.4:c.1774+2_1774+7del
ENST00000612417.4:c.1711+2_1711+7del
ENST00000621016.4:c.1711+2_1711+7del
NM_004360.3:c.1711+2_1711+7del
NM_001317184.1:c.1528+2_1528+7del
NM_001317185.1:c.163+2_163+7del
NM_001317186.1:c.-254-2574_-254-2569del
NM_004360.5:c.1711+2_1711+7del
NM_001317184.2:c.1528+2_1528+7del
NM_001317185.2:c.163+2_163+7del
NM_001317186.2:c.-254-2574_-254-2569del
NM_004360.5(CDH1):c.1711+2_1711+7del

Likely Pathogenic

Met criteria codes 4
PVS1_Strong PS4_Supporting PM2_Supporting PM5_Supporting
Not Met criteria codes 22
PM3 PM1 PM4 PS2 PS3 PS1 PM6 BA1 BP2 BP3 BP4 BP1 BP5 BP7 BS2 BS4 BS3 BS1 PP1 PP4 PP3 PP2

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.1711+2_1711+7delTAAGGG variant is a canonical splice variant predicted to result in a truncated or absent protein (PVS1_Strong, PM5_Supporting). This variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). The variant has been reported in at least one family meeting HDGC clinical criteria (PS4_Supporting; SCV000217020.4). In summary, 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 (Variant Interpretation Guidelines Version 3.1): PVS1_Strong, PM2_Supporting, PS4_Supporting, PM5_Supporting.
Met criteria codes
PVS1_Strong
A 6 bp deletion including +2 of the canonical donor splice site in intron 11, which is predicted to result in a truncated or loss of the protein
PS4_Supporting
One family meets HDGC clinical criteria (SCV000217020.4).
PM2_Supporting
Absent in gnomAD
PM5_Supporting
Apply PM5_Supporting to the variant with the alteration at canonical splicing site.
Not Met criteria codes
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
PS2
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
PM6
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
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
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
BP5
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
BS2
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
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
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
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
Approved on: 2023-08-24
Published on: 2023-08-24
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