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

UUID: 4de15575-228f-4350-8bab-2e2dbfd23694

Approved on: 2023-08-10

Published on: 2023-08-10

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: BS2 BS1

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

Expert Panel

CDH1 VCEP

Criteria Specification Information

Criteria Specification: ClinGen CDH1 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 3.1

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

• BS2: Observed in 61 individuals w/o dx of HDGC
• BS1: The "other" population in gnomAD meets criteria.

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
• 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
• 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
• 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: The "other" population in gnomAD meets criteria.
• 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
• 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