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_004360.4(CDH1):c.2324delG (p.Gly775Alafs)

CA16615415

406669 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 07bc6bc1-21bc-476e-bab1-e1fc34001d34
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.4:c.2324del
NM_004360.4(CDH1):c.2324delG (p.Gly775Alafs)
NC_000016.10:g.68829682del
CM000678.2:g.68829682del
NC_000016.9:g.68863585del
CM000678.1:g.68863585del
NC_000016.8:g.67421086del
NG_008021.1:g.97391del
ENST00000261769.10:c.2324del
ENST00000261769.9:c.2324del
ENST00000422392.6:c.2141del
ENST00000562118.1:n.542del
ENST00000562836.5:n.2395del
ENST00000566510.5:c.*990del
ENST00000566612.5:c.*564del
ENST00000611625.4:c.2387del
ENST00000612417.4:c.1853+3128del
ENST00000621016.4:c.1866-4521del
NM_004360.3:c.2324del
NM_001317184.1:c.2141del
NM_001317185.1:c.776del
NM_001317186.1:c.359del
NM_004360.5:c.2324del
NM_001317184.2:c.2141del
NM_001317185.2:c.776del
NM_001317186.2:c.359del
NM_004360.5(CDH1):c.2324del (p.Gly775fs)
More

Pathogenic

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

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.2324delG (p.Gly775Alafs) 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
A 1 bp deletion in exon 15/16, predicted to result in a premature termination codon that leads to NMD
PVS1
A 1 bp deletion in exon 15/16, predicted to result in a premature termination codon that leads to NMD
PM2_Supporting
Absent in gnomAD
Not Met criteria codes
BA1
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
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
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
PS4
Proband does not fulfil HDGC clinical criteria, because pathology is not available (SCV000545472.2)
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
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
Two meioses across one family (SCV000545472.2).
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
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
PM3
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
Curation History
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