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]
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Variant: NM_004360.5(CDH1):c.161G>A (p.Arg54Lys)

CA10580076

230641 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: e2d97b1d-834f-46eb-af22-42a683692c77
Approved on: 2023-08-02
Published on: 2023-08-02

HGVS expressions

NM_004360.5:c.161G>A
NM_004360.5(CDH1):c.161G>A (p.Arg54Lys)
NC_000016.10:g.68738409G>A
CM000678.2:g.68738409G>A
NC_000016.9:g.68772312G>A
CM000678.1:g.68772312G>A
NC_000016.8:g.67329813G>A
NG_008021.1:g.6118G>A
ENST00000261769.10:c.161G>A
ENST00000261769.9:c.161G>A
ENST00000422392.6:c.161G>A
ENST00000566510.5:c.161G>A
ENST00000566612.5:c.161G>A
ENST00000611625.4:c.161G>A
ENST00000612417.4:c.161G>A
ENST00000621016.4:c.161G>A
NM_004360.3:c.161G>A
NM_001317184.1:c.161G>A
NM_001317185.1:c.-1455G>A
NM_001317186.1:c.-1659G>A
NM_004360.4:c.161G>A
NM_001317184.2:c.161G>A
NM_001317185.2:c.-1455G>A
NM_001317186.2:c.-1659G>A

Likely Benign

Met criteria codes 2
PM2_Supporting BS2
Not Met criteria codes 24
BS4 BS3 BS1 BP5 BP7 BP2 BP3 BP4 BP1 PVS1 PM6 PS1 PS2 PS4 PS3 BA1 PM5 PM3 PM1 PM4 PP4 PP1 PP3 PP2

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.161G>A (p.Arg54Lys) missense variant is absent in the gnomAD 2.1.1 cohort (PM2_supporting; http://gnomad.broadinstitute.org). This variant has been observed in ≥10 individuals without DGC, SRC tumours or LBC and whose families do not suggest HDGC (BS2; SCV000274257.4, SCV000637737.4, unpublished data). In summary, although a conflicting code PM2_supporting is met, this variant meets criteria to be classified as likely benign based on ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel: PM2_supporting, BS2. (CDH1 VCEP specifications version 3.1; 04/24/2023)
Met criteria codes
PM2_Supporting
Absent in gnomAD v2.1.1
BS2
Variant seen in >= 10 individuals w/o DGC, SRC tumors, or LBC & whose families do not suggest HDGC
Not Met criteria codes
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
absent in gnomAD
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
PVS1
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
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
PS4
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
BA1
absent in gnomAD
PM5
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
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
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
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