U.S. flag

An official website of the United States government

NM_004360.5(CDH1):c.2440-2A>G AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 30, 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:
RCV003328436.4

Allele description [Variation Report for NM_004360.5(CDH1):c.2440-2A>G]

NM_004360.5(CDH1):c.2440-2A>G

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.2440-2A>G
HGVS:
  • NC_000016.10:g.68833288A>G
  • NG_008021.1:g.100997A>G
  • NM_001317184.2:c.2257-2A>G
  • NM_001317185.2:c.892-2A>G
  • NM_001317186.2:c.475-2A>G
  • NM_004360.4(CDH1):c.2440-2A>G
  • NM_004360.5:c.2440-2A>GMANE SELECT
  • LRG_301t1:c.2440-2A>G
  • LRG_301:g.100997A>G
  • NC_000016.9:g.68867191A>G
  • NM_004360.3:c.2440-2A>G
  • NM_004360.4(CDH1):c.2440-2A>G
  • NM_004360.4:c.2440-2A>G
Links:
dbSNP: rs1555518210
NCBI 1000 Genomes Browser:
rs1555518210
Molecular consequence:
  • NM_001317184.2:c.2257-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001317185.2:c.892-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001317186.2:c.475-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_004360.5:c.2440-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV001142259ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Likely pathogenic
(Aug 30, 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, SCV001142259.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.2440-2A>G variant is a canonical splice variant predicted to result in a truncated or absent protein (PVS1_Strong, PM5_Supporting). This variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). There is also an RNA assay demonstrating abnormal splicing (PS3_Moderate; SCV000700319.2). In summary, this variant meets criteria to be classified as likely pathogenic based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): PVS1_strong, PM2_Supporting, PS3_Moderate, PM5_Supporting.

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

Last Updated: Nov 3, 2024