NM_004360.5(CDH1):c.49-3C>T AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 17, 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:
RCV003328222.2

Allele description [Variation Report for NM_004360.5(CDH1):c.49-3C>T]

NM_004360.5(CDH1):c.49-3C>T

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.49-3C>T
HGVS:
  • NC_000016.10:g.68738294C>T
  • NG_008021.1:g.6003C>T
  • NM_001317184.2:c.49-3C>T
  • NM_001317185.2:c.-1567-3C>T
  • NM_001317186.2:c.-1771-3C>T
  • NM_004360.5:c.49-3C>TMANE SELECT
  • LRG_301t1:c.49-3C>T
  • LRG_301:g.6003C>T
  • NC_000016.9:g.68772197C>T
  • NM_004360.3:c.49-3C>T
  • NM_004360.5(CDH1):c.49-3C>TMANE SELECT
Links:
dbSNP: rs587782366
NCBI 1000 Genomes Browser:
rs587782366
Molecular consequence:
  • NM_001317184.2:c.49-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317185.2:c.-1567-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317186.2:c.-1771-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004360.5:c.49-3C>T - intron variant - [Sequence Ontology: SO:0001627]

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

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001244345ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Likely benign
(Aug 17, 2023) 		germlinecuration

Citation Link

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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, SCV001244345.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.49-3C>T variant has been observed in at least 10 individuals without DGC, SRC tumours, or LBC & whose families do not suggest HDGC (BS2; SCV000186304.5, SCV000288486.4). There are at least 3 in silico predictors in agreement that this variant does not affect splicing (BP4). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BS2, BP4.

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

Last Updated: Feb 28, 2024