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
  • No ClinVar Id was directly found from the curated document
  • ClinVar Id was derived from the Allele Registry.

Variant: NM_001317186.2:c.-1818T>A

CA396451188

1292057 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 4298342a-f7ef-461f-bdcb-ce5a49048165
Approved on: 2023-08-25
Published on: 2023-08-25

HGVS expressions

NM_001317186.2:c.-1818T>A
NC_000016.10:g.68737417T>A
CM000678.2:g.68737417T>A
NC_000016.9:g.68771320T>A
CM000678.1:g.68771320T>A
NC_000016.8:g.67328821T>A
NG_008021.1:g.5126T>A
ENST00000261769.10:c.2T>A
ENST00000261769.9:c.2T>A
ENST00000422392.6:c.2T>A
ENST00000566510.5:c.2T>A
ENST00000566612.5:c.2T>A
ENST00000611625.4:c.2T>A
ENST00000612417.4:c.2T>A
ENST00000621016.4:c.2T>A
NM_004360.3:c.2T>A
NM_001317184.1:c.2T>A
NM_001317185.1:c.-1614T>A
NM_001317186.1:c.-1818T>A
NM_004360.4:c.2T>A
NM_004360.5:c.2T>A
NM_001317184.2:c.2T>A
NM_001317185.2:c.-1614T>A
NM_004360.5(CDH1):c.2T>A (p.Met1Lys)

Pathogenic

Met criteria codes 3
PS4_Supporting PVS1 PM2_Supporting
Not Met criteria codes 23
BA1 PS1 PS3 PS2 PP3 PP2 PP4 PP1 PM6 PM1 PM4 PM5 PM3 BS3 BS4 BS1 BS2 BP7 BP5 BP3 BP4 BP1 BP2

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.2T>A (p.Met1?) variant alters the start codon of the CDH1 coding sequence and is predicted to lead to an absent protein (PVS1). This variant is absent in the gnomAD cohort (PM2_supporting; http://gnomad.broadinstitute.org). This variant has been reported in at least one proband meeting HDGC clinical criteria (PS4_supporting; Internal laboratory contributor). In summary, this variant meets criteria to be classified as pathogenic based on the ACMG/AMP Variant Interpretation Guidelines Version 3.1 as specified by the CDH1 Variant Curation Expert Panel: PVS1, PM2_supporting, PS4_supporting.
Met criteria codes
PS4_Supporting
One proband meet HDGC phenotype criteria (Internal laboratory contributor).
PVS1
PVS1 applies to initiation codon variants
PM2_Supporting
Absent from all population databases
Not Met criteria codes
BA1
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
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
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
PM5
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
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
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
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