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NM_004360.5(CDH1):c.387+6T>C 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:
RCV003328337.2

Allele description [Variation Report for NM_004360.5(CDH1):c.387+6T>C]

NM_004360.5(CDH1):c.387+6T>C

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.387+6T>C
HGVS:
  • NC_000016.10:g.68801899T>C
  • NG_008021.1:g.69608T>C
  • NM_001317184.2:c.387+6T>C
  • NM_001317185.2:c.-1229+6T>C
  • NM_001317186.2:c.-1433+6T>C
  • NM_004360.5:c.387+6T>CMANE SELECT
  • LRG_301t1:c.387+6T>C
  • LRG_301:g.69608T>C
  • NC_000016.9:g.68835802T>C
  • NM_004360.3:c.387+6T>C
  • NM_004360.4:c.387+6T>C
Links:
dbSNP: rs764434962
NCBI 1000 Genomes Browser:
rs764434962
Molecular consequence:
  • NM_001317184.2:c.387+6T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317185.2:c.-1229+6T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317186.2:c.-1433+6T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004360.5:c.387+6T>C - 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
SCV001943362ClinGen 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, SCV001943362.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

c.387+6T>C is an intronic variant in the splice donor region of intron 3. This variant has an allele frequency of 0.0001 (5/34548 alleles) in the gnomAD v2.1 Latino/admixed American sub-population (http://gnomad.broadinstitute.org). This variant has been reported in at least 13 individuals without DGC, SRC tumours or LBC and whose families do not suggest HDGC (BS2; SCV000637825.4). This variant is predicted to have no impact on splicing by multiple in silico splice site predictors (BP4; SpliceAI, varSEAK, MaxEntScan). In summary, this variant meets criteria to be classified as likely benign based on 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: Sep 29, 2024