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]
Link to SEPIO compliant JSON-LD document

Variant: NM_004360.5(CDH1):c.546A>C (p.Lys182Asn)

CA163740

140853 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 4dbe4a4e-01f1-4566-96b5-4c9d2a05ba36
Approved on: 2023-08-10
Published on: 2023-08-10

HGVS expressions

NM_004360.5:c.546A>C
NM_004360.5(CDH1):c.546A>C (p.Lys182Asn)
NC_000016.10:g.68808707A>C
CM000678.2:g.68808707A>C
NC_000016.9:g.68842610A>C
CM000678.1:g.68842610A>C
NC_000016.8:g.67400111A>C
NG_008021.1:g.76416A>C
ENST00000261769.10:c.546A>C
ENST00000261769.9:c.546A>C
ENST00000422392.6:c.546A>C
ENST00000561751.1:n.313A>C
ENST00000562836.5:n.617A>C
ENST00000564676.5:n.828A>C
ENST00000564745.1:n.541A>C
ENST00000566510.5:c.531+140A>C
ENST00000566612.5:c.546A>C
ENST00000567320.1:n.56A>C
ENST00000611625.4:c.546A>C
ENST00000612417.4:c.546A>C
ENST00000621016.4:c.546A>C
NM_004360.3:c.546A>C
NM_001317184.1:c.546A>C
NM_001317185.1:c.-1070A>C
NM_001317186.1:c.-1274A>C
NM_004360.4:c.546A>C
NM_001317184.2:c.546A>C
NM_001317185.2:c.-1070A>C
NM_001317186.2:c.-1274A>C

Benign

Met criteria codes 2
BS1 BS2
Not Met criteria codes 24
PVS1 BA1 BS4 BS3 BP7 BP5 BP2 BP3 BP4 BP1 PS4 PS2 PS1 PS3 PP4 PP3 PP2 PP1 PM5 PM1 PM3 PM4 PM6 PM2

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.546A>C (p.Lys182Asn) variant has an allele frequency of 0.00104 (>0.1%, 9 out of 8628 alleles) in the East Asian subpopulation of the ExAC cohort (BS1). The variant has also been observed in >10 (56) individuals without a diagnosis of diffuse gastric cancer, signet ring tumor or lobular breast cancer and whose family histories do not suggest HDGC (BS2; SCV000637839.5; SCV000566004.5). Therefore, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BS1, BS2.
Met criteria codes
BS1
MAF is 0.00104 (9 out of 8628 alleles) in East Asian population of ExAC population database which is higher than BS1 cutoff 0.1%
BS2
Variant seen in >10 (56) individuals w/o DCG, SRC tumors, or LBC & whose families do not suggest HDGC.
Not Met criteria codes
PVS1
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
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
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
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
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
PS3
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
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
PM5
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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