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_004360.4(CDH1):c.188G>A (p.Arg63Gln)

CA288048

127919 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 4de15575-228f-4350-8bab-2e2dbfd23694

HGVS expressions

NM_004360.4:c.188G>A
NM_004360.4(CDH1):c.188G>A (p.Arg63Gln)
NC_000016.10:g.68801694G>A
CM000678.2:g.68801694G>A
NC_000016.9:g.68835597G>A
CM000678.1:g.68835597G>A
NC_000016.8:g.67393098G>A
NG_008021.1:g.69403G>A
ENST00000261769.10:c.188G>A
ENST00000261769.9:c.188G>A
ENST00000422392.6:c.188G>A
ENST00000562836.5:n.259G>A
ENST00000564676.5:n.470G>A
ENST00000564745.1:n.183G>A
ENST00000566510.5:c.188G>A
ENST00000566612.5:c.188G>A
ENST00000611625.4:c.188G>A
ENST00000612417.4:c.188G>A
ENST00000621016.4:c.188G>A
NM_004360.3:c.188G>A
NM_001317184.1:c.188G>A
NM_001317185.1:c.-1428G>A
NM_001317186.1:c.-1632G>A
NM_004360.5:c.188G>A
NM_001317184.2:c.188G>A
NM_001317185.2:c.-1428G>A
NM_001317186.2:c.-1632G>A
NM_004360.5(CDH1):c.188G>A (p.Arg63Gln)

Benign

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

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.188G>A (p.Arg63Gln) variant has an allele frequency of 0.00109 (0.11%, 6/5486 alleles) in the “Other” subpopulation of the gnomAD cohort (BS1). This variant has also been observed in >10 without a diagnosis of diffuse gastric cancer, signet ring tumor or lobular breast cancer and whose family histories do not suggest HDGC (BS2; internal laboratory contributors). In summary, 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
The "other" population in gnomAD meets criteria.
BS2
Observed in 61 individuals w/o dx of HDGC
Not Met criteria codes
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
The "other" population in gnomAD meets criteria.
PVS1
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
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
The "other" population in gnomAD meets criteria.
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
It has seen co-occurrence with a mutation in another gene that clearly explains a proband's phenotype.
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
BP1
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
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
PS1
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
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
Approved on: 2023-08-10
Published on: 2023-08-10
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