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+1G>A

CA396465476

428628 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 35f43e27-91c5-4b71-a8e1-136519f0106b
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.4:c.1711+1G>A
NM_004360.4(CDH1):c.1711+1G>A
NC_000016.10:g.68819426G>A
CM000678.2:g.68819426G>A
NC_000016.9:g.68853329G>A
CM000678.1:g.68853329G>A
NC_000016.8:g.67410830G>A
NG_008021.1:g.87135G>A
ENST00000261769.10:c.1711+1G>A
ENST00000261769.9:c.1711+1G>A
ENST00000422392.6:c.1528+1G>A
ENST00000562836.5:n.1782+1G>A
ENST00000566510.5:c.*377+1G>A
ENST00000566612.5:c.1566-2575G>A
ENST00000611625.4:c.1774+1G>A
ENST00000612417.4:c.1711+1G>A
ENST00000621016.4:c.1711+1G>A
NM_004360.3:c.1711+1G>A
NM_001317184.1:c.1528+1G>A
NM_001317185.1:c.163+1G>A
NM_001317186.1:c.-254-2575G>A
NM_004360.5:c.1711+1G>A
NM_001317184.2:c.1528+1G>A
NM_001317185.2:c.163+1G>A
NM_001317186.2:c.-254-2575G>A
NM_004360.5(CDH1):c.1711+1G>A

Likely Pathogenic

Met criteria codes 3
PVS1_Strong PM2_Supporting PM5_Supporting
Not Met criteria codes 23
BS3 BS4 BS1 BS2 BP5 BP7 BP2 BP3 BP4 BP1 PS3 PS2 PS1 PS4 PM6 PM3 PM1 PM4 PP4 PP1 PP3 PP2 BA1

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.1711+1G>A variant is a canonical splice variant predicted to result in a truncated or absent protein (PVS1_Strong). The variant is absent in the gnomAD cohort. (PM2_Supporting; http://gnomad.broadinstitute.org). This variant is at +1 donor site variant with other likely pathogenic canonical splicing variants curated at the same splice site (PM5_Supporting). Therefore, 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, PM2_Supporting, PM5_Supporting.
Met criteria codes
PVS1_Strong
Canonical +1 splice site variant in intron 11, predicted to affect the donor site leading to truncated or absent protein. There are no predicted cryptic splice sites nearby.
PM2_Supporting
Absent in gnomAD cohort.
PM5_Supporting
GT-AG 1,2 acceptor/donor site variant with other Likely Pathogenic variants curated at the same splice site.
Not Met criteria codes
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
BS2
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
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
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
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Proband with no further information (PMID: 28152038). SCV000817795.1 - One family meet HDGC clinical criteria.
Hereditary cancer-predisposing syndrome proband with no other information. Also submitted to ClinVar - SCV000580706. PubMed:28152038
PM6
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
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
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
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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