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NM_004360.5(CDH1):c.49-8C>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:
RCV003328338.2

Allele description [Variation Report for NM_004360.5(CDH1):c.49-8C>T]

NM_004360.5(CDH1):c.49-8C>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.49-8C>T
HGVS:
  • NC_000016.10:g.68738289C>T
  • NG_008021.1:g.5998C>T
  • NM_001317184.2:c.49-8C>T
  • NM_001317185.2:c.-1567-8C>T
  • NM_001317186.2:c.-1771-8C>T
  • NM_004360.4(CDH1):c.49-8C>T
  • NM_004360.5:c.49-8C>TMANE SELECT
  • LRG_301t1:c.49-8C>T
  • LRG_301:g.5998C>T
  • NC_000016.9:g.68772192C>T
  • NM_004360.3:c.49-8C>T
  • NM_004360.4(CDH1):c.49-8C>T
  • NM_004360.4:c.49-8C>T
Links:
dbSNP: rs774761552
NCBI 1000 Genomes Browser:
rs774761552
Molecular consequence:
  • NM_001317184.2:c.49-8C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317185.2:c.-1567-8C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317186.2:c.-1771-8C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004360.5:c.49-8C>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
SCV001142213ClinGen 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, SCV001142213.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.49-8C>T is an intronic variant in the splice acceptor region of intron 1. This variant has an allele frequency of 0.00001 (2/150178) in gnomAD with a maximum frequency of 0.00003 (2/57282) in the European (Non-Finnish) sub-population. This variant has been reported in at least 12 individuals without DGC, SRC tumours or LBC and whose families do not suggest HDGC (BS2; SCV000529519.4, SCV000557406.3). This variant is predicted to have no impact on splicing by multiple in silico splice site predictors. HumanSpliceFinder predicts that this variant may create an exonic ESS site, but this effect has not been demonstrated experimentally to our knowledge (BP4). 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