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NM_004360.5(CDH1):c.1566-1G>C AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 21, 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:
RCV003328415.2

Allele description [Variation Report for NM_004360.5(CDH1):c.1566-1G>C]

NM_004360.5(CDH1):c.1566-1G>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.1566-1G>C
HGVS:
  • NC_000016.10:g.68819279G>C
  • NG_008021.1:g.86988G>C
  • NM_001317184.2:c.1383-1G>C
  • NM_001317185.2:c.18-1G>C
  • NM_001317186.2:c.-254-2722G>C
  • NM_004360.5:c.1566-1G>CMANE SELECT
  • LRG_301t1:c.1566-1G>C
  • LRG_301:g.86988G>C
  • NC_000016.9:g.68853182G>C
  • NC_000016.9:g.68853182G>C
  • NM_004360.3:c.1566-1G>C
  • NM_004360.4:c.1566-1G>C
Links:
dbSNP: rs113583899
NCBI 1000 Genomes Browser:
rs113583899
Molecular consequence:
  • NM_001317186.2:c.-254-2722G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317184.2:c.1383-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001317185.2:c.18-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_004360.5:c.1566-1G>C - 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

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001943358ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Uncertain significance
(Aug 21, 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, SCV001943358.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.1566-1G>C variant is a canonical splice variant predicted to result in the use of a cryptic splice site which preserves the reading frame (PVS1_moderate). This variant is absent in the gnomAD v2.1.1 cohort. In the gnomAD v3 it has a frequency of 0.000006978 (1 of 143,302) with a maximum non-founder allele frequency of 0.00001549 (1 of 64,570) in the European non-Finnish subpopulation (PM2_supporting; http://gnomad.broadinstitute.org). The variant has been reported in two families meeting clinical criteria for HDGC (PS4_moderate, SCV000666335.2, internal laboratory contributor). In summary, the clinical significance of this variant is classified as of uncertain significance based the ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): PVS1_moderate, PS4_moderate, PM2_supporting.

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

Last Updated: Sep 29, 2024