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Please note this is a beta version of the ClinGen Evidence Repository. This resource is intended to provide access to variant level evidence used and applied by ClinGen Variant Curation Expert Panels in the classification of variants. In this beta version, the evidence is limited to curation notes and referenced literature (PMIDs).

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Criteria Specification: CSpec Registry PDF

Variant: NM_004360.5(CDH1):c.692_693TC[2] (p.His233fs)

CA16614952

406615 (ClinVar)

Gene: CDH1
Condition: hereditary diffuse gastric cancer
Inheritance Mode: Autosomal dominant inheritance

HGVS expressions

NM_004360.5:c.692_693TC[2]
NM_004360.5(CDH1):c.692_693TC[2] (p.His233fs)
ENST00000261769.10:c.692_693del
ENST00000261769.9:c.692_693del
ENST00000422392.6:c.692_693del
ENST00000566510.5:c.536_537del
ENST00000566612.5:c.692_693del
ENST00000611625.4:c.692_693del
ENST00000612417.4:c.692_693del
ENST00000621016.4:c.692_693del
NM_004360.3:c.692_693del
NM_001317184.1:c.692_693del
NM_001317185.1:c.-924_-923del
NM_001317186.1:c.-1128_-1127del
NM_004360.4:c.692_693del
NM_004360.5:c.692_693del
NM_001317184.2:c.692_693del
NM_001317185.2:c.-924_-923del
NM_001317186.2:c.-1128_-1127del
NC_000016.10:g.68810201_68810202del
CM000678.2:g.68810201_68810202del
NC_000016.9:g.68844104_68844105del
CM000678.1:g.68844104_68844105del
NC_000016.8:g.67401605_67401606del
NG_008021.1:g.77910_77911del

Pathogenic

Met criteria codes 3
PVS1 PM5_Supporting PM2_Supporting
Unmet criteria codes 23
PM6 PM4 PM1 PM3 BA1 BS3 BS4 BS1 BS2 BP7 BP5 BP3 BP4 BP1 BP2 PS1 PS3 PS2 PS4 PP3 PP2 PP1 PP4

Expert Panel

Evidence Links 0

Evidence submitted by expert panel
CDH1 VCEP
The c.696_697delTC p.(His233fs) variant is predicted to result in a premature stop codon that leads to nonsense mediate decay (PVS1 and PM5_supporting). This 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
Exon 6 of 16, predicted NMD.
PM5_Supporting
Exon 6 of 16, predicted NMD.
PM2_Supporting
Absent in population databases.
Unmet criteria codes
PM6
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
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
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
SCV000545369.3 - family history 2 cases stomach cancer (no pathology provided).
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: 2021-05-05
Published on: 2021-05-05
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