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]
  • See Evidence submitted by expert panel for details.

Variant: NM_004360.4(CDH1):c.2324delG (p.Gly775Alafs)

CA16615415

406669 (ClinVar)

Gene: CDH1
Condition: hereditary diffuse gastric cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 07bc6bc1-21bc-476e-bab1-e1fc34001d34
Approved on: 2021-05-05
Published on: 2021-05-05

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
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Pathogenic

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

Evidence Links 0

Expert Panel

Criteria Specification Information

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). In summary, 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 (Variant Interpretation Guidelines Version 3): PVS1, PM2_supporting, PM5_supporting.
Met criteria codes
PVS1
A 1 bp deletion in exon 15/16, predicted to result in a premature termination codon that leads to NMD
PM5_Supporting
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
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
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
BS2
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
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
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
BP4
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
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
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
PS4
Proband does not fulfil HDGC clinical criteria, because pathology is not available (SCV000545472.2)
PP1
Two meioses across one family (SCV000545472.2).
PP2
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
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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