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.1505del (p.Gly502fs)

CA353528

224529 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: fded881f-0be4-437b-b405-09f55bcc74d5
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.5:c.1505del
NM_004360.5(CDH1):c.1505del (p.Gly502fs)
NC_000016.10:g.68815699del
CM000678.2:g.68815699del
NC_000016.9:g.68849602del
CM000678.1:g.68849602del
NC_000016.8:g.67407103del
NG_008021.1:g.83408del
ENST00000261769.10:c.1505del
ENST00000261769.9:c.1505del
ENST00000422392.6:c.1322del
ENST00000562836.5:n.1576del
ENST00000566510.5:c.*171del
ENST00000566612.5:c.1505del
ENST00000611625.4:c.1568del
ENST00000612417.4:c.1505del
ENST00000621016.4:c.1505del
NM_004360.3:c.1505del
NM_001317184.1:c.1322del
NM_001317185.1:c.-44del
NM_001317186.1:c.-315del
NM_004360.4:c.1505del
NM_001317184.2:c.1322del
NM_001317185.2:c.-44del
NM_001317186.2:c.-315del
More

Pathogenic

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

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.1505del (p.Gly502fs) 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
PM5_Supporting
Variant predicted to result in NMD with position of stop codon at aa 521
PVS1
Variant predicted to result in NMD with position of stop codon at aa 521
PM2_Supporting
Variant is absent in gnomAD
Not Met criteria codes
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
PS4
This variant has been reported in an individual with a personal and family history of breast cancer (pathology unknown)
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
BP3
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
BA1
Variant is absent in gnomAD
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
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
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
Variant is absent in gnomAD
Curation History
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