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.2076T>C (p.Ala692=)

CA169363

142770 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 7147ec7b-30b2-419d-9646-4283a89cbe74

HGVS expressions

NM_004360.5:c.2076T>C
NM_004360.5(CDH1):c.2076T>C (p.Ala692=)
NC_000016.10:g.68823538T>C
CM000678.2:g.68823538T>C
NC_000016.9:g.68857441T>C
CM000678.1:g.68857441T>C
NC_000016.8:g.67414942T>C
NG_008021.1:g.91247T>C
ENST00000261769.10:c.2076T>C
ENST00000261769.9:c.2076T>C
ENST00000422392.6:c.1893T>C
ENST00000562118.1:n.294T>C
ENST00000562836.5:n.2147T>C
ENST00000566510.5:c.*742T>C
ENST00000566612.5:c.*316T>C
ENST00000611625.4:c.2139T>C
ENST00000612417.4:c.1830+1419T>C
ENST00000621016.4:c.1865+1384T>C
NM_004360.3:c.2076T>C
NM_001317184.1:c.1893T>C
NM_001317185.1:c.528T>C
NM_001317186.1:c.111T>C
NM_004360.4:c.2076T>C
NM_001317184.2:c.1893T>C
NM_001317185.2:c.528T>C
NM_001317186.2:c.111T>C

Benign

Met criteria codes 2
BA1 BP2
Not Met criteria codes 24
PVS1 BS2 BS3 BS4 BS1 BP3 BP4 BP1 BP7 BP5 PS3 PS1 PS2 PS4 PP3 PP2 PP1 PP4 PM4 PM1 PM5 PM3 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 NM_004360.5(CDH1):c.2076T>C (p.Ala692=) variant has an allele frequency of 0.88894 (88.89%, 22156/24924 alleles, 9856 homozygotes) in the African subpopulation of the gnomAD v2.1.1 cohort (BA1; BP2_Supporting). 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): BA1, BP2_Supporting.
Met criteria codes
BA1
MAF > 0.2%: African AF is 0.88894 (22156/24924 alleles, 9856 homozygotes in gnomAD v2.1.1)
BP2
9856 Africa homozygotes in the controls cohort in gnomAD v2.1.1
Not Met criteria codes
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
Not assessed, because BA1 met
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
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
Not assessed, because BA1 met
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
Not assessed, because BA1 met
BP5
Not assessed, because BA1 met
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
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
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
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
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
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
Approved on: 2023-08-09
Published on: 2023-08-10
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