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.2296-1G>A

CA16042157

371806 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 62569505-a102-4142-ab42-cedf24c4765b
Approved on: 2023-08-24
Published on: 2023-08-24

HGVS expressions

NM_004360.5:c.2296-1G>A
NM_004360.5(CDH1):c.2296-1G>A
NC_000016.10:g.68829653G>A
CM000678.2:g.68829653G>A
NC_000016.9:g.68863556G>A
CM000678.1:g.68863556G>A
NC_000016.8:g.67421057G>A
NG_008021.1:g.97362G>A
ENST00000261769.10:c.2296-1G>A
ENST00000261769.9:c.2296-1G>A
ENST00000422392.6:c.2113-1G>A
ENST00000562118.1:n.514-1G>A
ENST00000562836.5:n.2367-1G>A
ENST00000566510.5:c.*962-1G>A
ENST00000566612.5:c.*536-1G>A
ENST00000611625.4:c.2359-1G>A
ENST00000612417.4:c.1853+3099G>A
ENST00000621016.4:c.1866-4550G>A
NM_004360.3:c.2296-1G>A
NM_001317184.1:c.2113-1G>A
NM_001317185.1:c.748-1G>A
NM_001317186.1:c.331-1G>A
NM_004360.4:c.2296-1G>A
NM_001317184.2:c.2113-1G>A
NM_001317185.2:c.748-1G>A
NM_001317186.2:c.331-1G>A
More

Likely Pathogenic

Met criteria codes 4
PS4_Moderate PM5_Supporting PVS1_Strong PM2_Supporting
Not Met criteria codes 22
BA1 PS2 PS3 PS1 PP4 PP1 PP3 PP2 PM3 PM1 PM4 PM6 BS2 BS4 BS3 BS1 BP2 BP3 BP4 BP1 BP5 BP7

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.2296-1G>A 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). This variant has been reported in at least three families meeting HDGC clinical criteria (PS4_moderate; SCV000580714.3). In summary, this variant meets criteria to be classified as likely 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, PS4_moderate, PM2_supporting, PM5_supporting.
Met criteria codes
PS4_Moderate
3 families that meet HDGC criteria (SCV000580714.3). 2 families that have insufficient information to determine if they meet HDCG criteria
PM5_Supporting
Apply PM5_Supporting to the variant with the alteration at canonical splicing site.
PVS1_Strong
Intron 14 canonical acceptor splice site variant. Predicted loss of native site and creation of de novo acceptor leading to 1 bp deletion. RNA studies not conducted.
PM2_Supporting
Absent in gnomAD v2.1 and v3.0, in a region of sufficient coverage
Not Met criteria codes
BA1
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
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
<3 (2) affected meioses in one family
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
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
PM6
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
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
Curation History
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