Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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Variant: NM_004360.5(CDH1):c.1684A>G (p.Thr562Ala)

CA166617

141854 (ClinVar)

Gene: CDH1

Condition: CDH1-related diffuse gastric and lobular breast cancer

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 77378953-408f-4bee-85e0-ebd5248943f7

HGVS expressions

NM_004360.5:c.1684A>G

NM_004360.5(CDH1):c.1684A>G (p.Thr562Ala)

NC_000016.10:g.68819398A>G

CM000678.2:g.68819398A>G

NC_000016.9:g.68853301A>G

CM000678.1:g.68853301A>G

NC_000016.8:g.67410802A>G

NG_008021.1:g.87107A>G

ENST00000261769.10:c.1684A>G

ENST00000261769.9:c.1684A>G

ENST00000422392.6:c.1501A>G

ENST00000562836.5:n.1755A>G

ENST00000566510.5:c.*350A>G

ENST00000566612.5:c.1566-2603A>G

ENST00000611625.4:c.1747A>G

ENST00000612417.4:c.1684A>G

ENST00000621016.4:c.1684A>G

NM_004360.3:c.1684A>G

NM_001317184.1:c.1501A>G

NM_001317185.1:c.136A>G

NM_001317186.1:c.-254-2603A>G

NM_004360.4:c.1684A>G

NM_001317184.2:c.1501A>G

NM_001317185.2:c.136A>G

NM_001317186.2:c.-254-2603A>G

Likely Benign

BS2

BA1 BS1 PM2

Evidence Links 0

Expert Panel

CDH1 VCEP

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.1684A>G (p.Thr562Ala) variant has been observed in >10 individuals 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, 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: BS2. (CDH1 VCEP specifications version 3.1; 06/26/2023)

BS2

This variant has been observed in 101 heterozygous individuals with no diffuse gastric cancer, signet ring cell carcinoma or lobular breast cancer and/or whose family histories do not suggest HDGC (BS2; GeneDX, Ambry, Invitae). Note that this includes one individual with family history of unspecified gastric cancer.

BA1

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

PM2

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

Approved on: 2023-08-03

Published on: 2023-08-03

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