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_004360.5(CDH1):c.11G>A (p.Trp4Ter)

CA396451240

918853 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 779fb7a8-6e03-4a37-bab2-3eee5f80110f

HGVS expressions

NM_004360.5:c.11G>A
NM_004360.5(CDH1):c.11G>A (p.Trp4Ter)
NC_000016.10:g.68737426G>A
CM000678.2:g.68737426G>A
NC_000016.9:g.68771329G>A
CM000678.1:g.68771329G>A
NC_000016.8:g.67328830G>A
NG_008021.1:g.5135G>A
ENST00000261769.10:c.11G>A
ENST00000261769.9:c.11G>A
ENST00000422392.6:c.11G>A
ENST00000566510.5:c.11G>A
ENST00000566612.5:c.11G>A
ENST00000611625.4:c.11G>A
ENST00000612417.4:c.11G>A
ENST00000621016.4:c.11G>A
NM_004360.3:c.11G>A
NM_001317184.1:c.11G>A
NM_001317185.1:c.-1605G>A
NM_001317186.1:c.-1809G>A
NM_004360.4:c.11G>A
NM_001317184.2:c.11G>A
NM_001317185.2:c.-1605G>A
NM_001317186.2:c.-1809G>A

Pathogenic

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

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.11G>A (p.Trp4Ter) 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
Creating a premature translation stop signal in codon 4 in exon 1 is expected to result in an absent or non-functional protein product
PM2_Supporting
absence in controls. not in gnomAD, 1000 genomics and ESP with adequate coverage.
PM5_Supporting
Creating a premature translation stop signal in codon 4 in exon 1 is expected to result in nonsense mediate decay.
Not Met criteria codes
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
PM1
Located in exon 1, the signal peptide.
PS1
.
PS4
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
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
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
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
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
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
Approved on: 2023-08-04
Published on: 2023-08-04
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