U.S. flag

An official website of the United States government

NM_004360.5(CDH1):c.120G>A (p.Thr40=) AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 18, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003328249.2

Allele description [Variation Report for NM_004360.5(CDH1):c.120G>A (p.Thr40=)]

NM_004360.5(CDH1):c.120G>A (p.Thr40=)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.120G>A (p.Thr40=)
HGVS:
  • NC_000016.10:g.68738368G>A
  • NG_008021.1:g.6077G>A
  • NM_001317184.2:c.120G>A
  • NM_001317185.2:c.-1496G>A
  • NM_001317186.2:c.-1700G>A
  • NM_004360.5:c.120G>AMANE SELECT
  • NP_001304113.1:p.Thr40=
  • NP_004351.1:p.Thr40=
  • LRG_301t1:c.120G>A
  • LRG_301:g.6077G>A
  • NC_000016.9:g.68772271G>A
  • NM_004360.3:c.120G>A
  • NM_004360.4:c.120G>A
  • NM_004360.5(CDH1):c.120G>AMANE SELECT
  • p.T40T
  • p.Thr40=
Links:
dbSNP: rs786201115
NCBI 1000 Genomes Browser:
rs786201115
Molecular consequence:
  • NM_001317185.2:c.-1496G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1700G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.120G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004360.5:c.120G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
CDH1-related diffuse gastric and lobular breast cancer syndrome
Synonyms:
CDH1-related diffuse gastric and lobular breast cancer
Identifiers:
MONDO: MONDO:0100488; MedGen: CN311521

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001365459ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Likely benign
(Aug 18, 2023) 		germlinecuration

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen CDH1 Variant Curation Expert Panel, SCV001365459.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.120G>A (p.Thr40=) variant results in a synonymous amino acid change in exon 2. Although this variant is absent from gnomAD (PM2_Supporting), it has been observed internally in at least three individuals without DGC, SRC tumours or LBC and whose families do not suggest HDGC (BS2_Supporting, SCV000214188.4, SCV001041247.2). In addition, this variant is not predicted to result in aberrant splicing and is not highly conserved (BP4, BP7). In summary, this variant meets criteria to be classified as likely benign based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BS2_supporting, BP4, BP7, PM2_Supporting.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024