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NM_004360.5(CDH1):c.4G>A (p.Gly2Ser) 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:
RCV003328247.2

Allele description [Variation Report for NM_004360.5(CDH1):c.4G>A (p.Gly2Ser)]

NM_004360.5(CDH1):c.4G>A (p.Gly2Ser)

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.4G>A (p.Gly2Ser)
HGVS:
  • NC_000016.10:g.68737419G>A
  • NG_008021.1:g.5128G>A
  • NM_001317184.2:c.4G>A
  • NM_001317185.2:c.-1612G>A
  • NM_001317186.2:c.-1816G>A
  • NM_004360.5:c.4G>AMANE SELECT
  • NP_001304113.1:p.Gly2Ser
  • NP_004351.1:p.Gly2Ser
  • LRG_301t1:c.4G>A
  • LRG_301:g.5128G>A
  • NC_000016.9:g.68771322G>A
  • NM_004360.3(CDH1):c.4G>A
  • NM_004360.3:c.4G>A
  • NM_004360.4:c.4G>A
  • p.G2S
  • p.Gly2Ser
Protein change:
G2S
Links:
dbSNP: rs786201212
NCBI 1000 Genomes Browser:
rs786201212
Molecular consequence:
  • NM_001317185.2:c.-1612G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1816G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.4G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.4G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001142269ClinGen 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, SCV001142269.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The CDH1 c.4G>A (p.Gly2Ser) missense variant has a frequency of 0.00002 (2 of 128,626) in gnomAD, with a maximum allele frequency of 0.00008 (2 of 24,378) in the Latino subpopulation (http://gnomad.broadinstitute.org). This variant has been observed in at least 10 individuals without DGC, SRC tumours or LBC and whose families do not suggest HDGC (BS2; unpublished). In summary, the clinical significance of this variant is classified as likely benign based on BS2 alone. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BS2.

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

Last Updated: Sep 29, 2024