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_004360.5(CDH1):c.269G>A (p.Arg90Gln)

CA169145

142692 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: d6a83f99-4418-4412-a73a-bedd91dad34c
Approved on: 2023-08-10
Published on: 2023-08-10

HGVS expressions

NM_004360.5:c.269G>A
NM_004360.5(CDH1):c.269G>A (p.Arg90Gln)
NC_000016.10:g.68801775G>A
CM000678.2:g.68801775G>A
NC_000016.9:g.68835678G>A
CM000678.1:g.68835678G>A
NC_000016.8:g.67393179G>A
NG_008021.1:g.69484G>A
ENST00000261769.10:c.269G>A
ENST00000261769.9:c.269G>A
ENST00000422392.6:c.269G>A
ENST00000561751.1:n.36G>A
ENST00000562836.5:n.340G>A
ENST00000564676.5:n.551G>A
ENST00000564745.1:n.264G>A
ENST00000566510.5:c.269G>A
ENST00000566612.5:c.269G>A
ENST00000611625.4:c.269G>A
ENST00000612417.4:c.269G>A
ENST00000621016.4:c.269G>A
NM_004360.3:c.269G>A
NM_001317184.1:c.269G>A
NM_001317185.1:c.-1347G>A
NM_001317186.1:c.-1551G>A
NM_004360.4:c.269G>A
NM_001317184.2:c.269G>A
NM_001317185.2:c.-1347G>A
NM_001317186.2:c.-1551G>A
More

Likely Benign

Met criteria codes 1
BS2
Not Met criteria codes 25
BS4 BS3 BS1 BP5 BP7 BP2 BP3 BP4 BP1 PS2 PS4 PS3 PS1 BA1 PVS1 PP1 PP4 PP3 PP2 PM3 PM1 PM4 PM5 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.269G>A (p.Arg90Gln) missense variant has a frequency of 0.00001989 (5 of 251,334) in the gnomAD v2.1.1 cohort, with a maximum non-founder allele frequency of 0.00004401 (5 of 113,622) in the European non-Finnish subpopulation (http://gnomad.broadinstitute.org). This variant has been observed in ≥10 (55) individuals without DGC, SRC tumours or LBC and whose families do not suggest HDGC (BS2; SCV000567761.3, SCV000254829.7). In summary, the clinical significance of this variant is classified as likely benign based on BS2 alone. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BS2.
Met criteria codes
BS2
Variant seen in >10 (55) individuals w/o DCG, SRC tumors, or LBC & whose families do not suggest HDGC (at least 50 cases between Invitae, GeneDx, Ambry)
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
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
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
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
BA1
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
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
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
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
frequency of 0.00001989 (5 of 251,334) in the gnomAD v2.1.1 cohort, with a maximum non-founder allele frequency of 0.00004401 (5 of 113,622) in the European non-Finnish subpopulation
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.