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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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NM_004360.4(CDH1):c.60G>A (p.Trp20Ter)

CA197127

187239 (ClinVar)

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

HGVS expressions

NM_004360.4:c.60G>A
NC_000016.10:g.68738308G>A
CM000678.2:g.68738308G>A
NC_000016.9:g.68772211G>A
CM000678.1:g.68772211G>A
NC_000016.8:g.67329712G>A
NG_008021.1:g.6017G>A
LRG_301:g.6017G>A
NM_004360.3:c.60G>A
LRG_301t1:c.60G>A
NM_001317184.1:c.60G>A
NM_001317185.1:c.-1556G>A
NM_001317186.1:c.-1760G>A
NM_004360.5:c.60G>A
ENST00000261769.9:c.60G>A
ENST00000422392.6:c.60G>A
ENST00000566510.5:c.60G>A
ENST00000566612.5:c.60G>A
ENST00000611625.4:c.60G>A
ENST00000612417.4:c.60G>A
ENST00000621016.4:c.60G>A
NM_004360.4(CDH1):c.60G>A (p.Trp20Ter)

Pathogenic

Met criteria codes 3
PVS1 PS4_Moderate PM2
Unmet criteria codes 16
BP5 BP7 BP2 BP4 PS1 PS3 PS2 PP1 PP3 PM6 PM4 BA1 BS3 BS4 BS1 BS2

Expert Panel

Evidence Links 2

Evidence submitted by expert panel
CDH1 VCEP
The c.60G>A (p.Trp20Ter) variant is predicted to result in a premature stop codon that leads to a truncated or absent protein (PVS1). This variant is absent in the gnomAD cohort (PM2; http://gnomad.broadinstitute.org). The variant has been reported in at least two families meeting HDGC clinical criteria (PS4_Moderate; PMID: 10072428, 28688938). 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: PVS1, PM2, PS4_Moderate.
Met criteria codes
PVS1
Nonsense variant
PS4_Moderate
Variant reported in 2 families meeting HDGC criteria

PM2
Not present in gnomAD
Unmet criteria codes
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
Not applicable
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
Not applicable
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No experiment studies published on this variant
PS2
Not reported de novo
PP1
Two meioses in one family (PMID: 10072428)
PP3
Not applicable
PM6
Not reported de novo
PM4
Not applicable
BA1
Not present in gnomAD
BS3
No experiment studies published on this variant
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
Not present in gnomAD
BS2
Not reported in unaffected individuals
Approved on: 2019-03-18
Published on: 2019-09-11
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