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NM_004360.5(CDH1):c.32TGC[7] (p.Leu14_Leu15dup) 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:
RCV003328224.2

Allele description [Variation Report for NM_004360.5(CDH1):c.32TGC[7] (p.Leu14_Leu15dup)]

NM_004360.5(CDH1):c.32TGC[7] (p.Leu14_Leu15dup)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.32TGC[7] (p.Leu14_Leu15dup)
HGVS:
  • NC_000016.10:g.68737447TGC[7]
  • NG_008021.1:g.5156TGC[7]
  • NM_001317184.2:c.32TGC[7]
  • NM_001317185.2:c.-1584TGC[7]
  • NM_001317186.2:c.-1788TGC[7]
  • NM_004360.5:c.32TGC[7]MANE SELECT
  • NP_001304113.1:p.Leu14_Leu15dup
  • NP_004351.1:p.Leu14_Leu15dup
  • LRG_301t1:c.41_46dup
  • LRG_301:g.5156TGC[7]
  • NC_000016.10:g.68737447_68737449TGC[7]
  • NC_000016.9:g.68771347_68771348insGCTGCT
  • NC_000016.9:g.68771350TGC[7]
  • NM_004360.3:c.41_46dup
  • NM_004360.3:c.41_46dupTGCTGC
  • NM_004360.4:c.32_46TGC[7]
  • NM_004360.4:c.41_46dup
  • NM_004360.5(CDH1):c.32_34TGC[7]MANE SELECT
  • NM_004360.5:c.41_46dupMANE SELECT
  • p.L14_L15dup
  • p.Leu14_Leu15dup
Links:
dbSNP: rs587782476
NCBI 1000 Genomes Browser:
rs587782476
Molecular consequence:
  • NM_001317185.2:c.-1584TGC[7] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1788TGC[7] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.32TGC[7] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_004360.5:c.32TGC[7] - inframe_insertion - [Sequence Ontology: SO:0001821]

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
SCV001365451ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Likely benign
(Aug 18, 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, SCV001365451.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.32_34TGC[7] (p.Leu14_Leu15dup) variant results in an in-frame insertion in exon 1. This variant has a frequency of 0.0008% in gnomAD (1 of 124,448) (PM2_Supporting; https://gnomad.broadinstitute.org/). However, this region has poor coverage and allele frequency estimates may not be reliable. This variant has also been identified in at least ten individuals without DGC, SRC tumours and LBC and whose families do not suggest HDGC (BS2, SCV000569203.4, SCV000186596.5, SCV000545430.4). 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, PM2_Supporting.

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

Last Updated: Sep 29, 2024