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]

Variant: NM_004360.4(CDH1):c.2413G>A (p.Asp805Asn)

CA157966

127925 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 8f3f955a-56d1-4528-83ec-f23b19eb3126
Approved on: 2023-08-08
Published on: 2023-08-08

HGVS expressions

NM_004360.4:c.2413G>A
NM_004360.4(CDH1):c.2413G>A (p.Asp805Asn)
NC_000016.10:g.68829771G>A
CM000678.2:g.68829771G>A
NC_000016.9:g.68863674G>A
CM000678.1:g.68863674G>A
NC_000016.8:g.67421175G>A
NG_008021.1:g.97480G>A
ENST00000261769.10:c.2413G>A
ENST00000261769.9:c.2413G>A
ENST00000422392.6:c.2230G>A
ENST00000562118.1:n.631G>A
ENST00000562836.5:n.2484G>A
ENST00000566510.5:c.*1079G>A
ENST00000566612.5:c.*653G>A
ENST00000611625.4:c.2476G>A
ENST00000612417.4:c.1853+3217G>A
ENST00000621016.4:c.1866-4432G>A
NM_004360.3:c.2413G>A
NM_001317184.1:c.2230G>A
NM_001317185.1:c.865G>A
NM_001317186.1:c.448G>A
NM_004360.5:c.2413G>A
NM_001317184.2:c.2230G>A
NM_001317185.2:c.865G>A
NM_001317186.2:c.448G>A
NM_004360.5(CDH1):c.2413G>A (p.Asp805Asn)
More

Benign

Met criteria codes 1
BA1
Not Met criteria codes 25
BS4 BS3 BS1 BS2 BP7 BP5 BP3 BP2 BP1 BP4 PS2 PS4 PS1 PS3 PP1 PP4 PP2 PP3 PM6 PM2 PM1 PM4 PM3 PM5 PVS1

Evidence Links 4

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.2413G>A (p.Asp805Asn) variant has an allele frequency of 0.00207 (0.21%, 21/10,148 alleles) in the Ashkenazi Jewish subpopulation of the gnomAD cohort (BA1). 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): BA1.
Met criteria codes
BA1
Gnomad: 0.2% (21 AJ alleles)
Not Met criteria codes
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
In vitro experiment showed that CHO cells transfected with this variant displayed smaller cellular aggregates than wildtype.
This variant was seen in one individual with an orofacial cleft. In vitro experiment showed that CHO cells transfected with this variant displayed smaller cellular aggregates than wildtype. PubMed:23197654
BS1
Gnomad: 0.2% (21 AJ alleles)
BS2
Variant reported in at least one healthy individual undergoing exome sequencing and at least one person undergoing testing for Lynch syndrome.
Variant reported in at least one healthy individual undergoing exome sequencing. PubMed:24728327
Reported in at least one individual undergoing testing for Lynch syndrome. PubMed:25980754
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
BP3
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
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
REVEL: 0.374 Align GVGD: Class C0
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
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
In vitro experiment showed that CHO cells transfected with this variant displayed smaller cellular aggregates than wildtype.
This variant was seen in one individual with an orofacial cleft. In vitro experiment showed that CHO cells transfected with this variant displayed smaller cellular aggregates than wildtype. PubMed:23197654
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
Variant seen in one unaffected proband whose mother had LBC at 45, maternal aunt had DGC at 55 and maternal uncle had GC at 69 but it is unknown whether they carried the variant. It was also seen in one Jewish proband with HDGC.
This variant was seen in one Jewish individual with HDGC. PubMed:26182300
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL: 0.374 Align GVGD: Class C0
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
Gnomad: 0.2% (21 AJ alleles)
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
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
Asp805Gly is VUS in clinvar.
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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