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
  • There was no gene found in the curated document received from the VCI/VCEP

Variant: NM_004360.4(CDH1):c.315delC (p.Thr106Profs)

CA16620235

422315 (ClinVar)

Gene: N/A
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 97caf259-aeae-41f1-b381-74069cc41be9

HGVS expressions

NM_004360.4(CDH1):c.315delC (p.Thr106Profs)
NC_000016.10:g.68801821del
CM000678.2:g.68801821del
NC_000016.9:g.68835724del
CM000678.1:g.68835724del
NC_000016.8:g.67393225del
NG_008021.1:g.69530del
ENST00000261769.10:c.315del
ENST00000261769.9:c.315del
ENST00000422392.6:c.315del
ENST00000561751.1:c.82del
ENST00000562836.5:n.386del
ENST00000564676.5:n.597del
ENST00000564745.1:n.310del
ENST00000566510.5:c.315del
ENST00000566612.5:c.315del
ENST00000611625.4:c.315del
ENST00000612417.4:c.315del
ENST00000621016.4:c.315del
NM_004360.3:c.315del
NM_001317184.1:c.315del
NM_001317185.1:c.-1301del
NM_001317186.1:c.-1505del
NM_004360.4:c.315del
NM_004360.5:c.315del
NM_001317184.2:c.315del
NM_001317185.2:c.-1301del
NM_001317186.2:c.-1505del
NM_004360.5(CDH1):c.315del (p.Thr106fs)

Pathogenic

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

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.315delC p.(Thr106Profs) 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
Predicted NMD.
PM5_Supporting
Predicted NMD.
PM2_Supporting
Not observed in 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
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
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
PS4
SCV000571755.3 - Proband does not meet HDGC clinical criteria. Not reported in the literature.
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
PM3
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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