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NM_004360.5(CDH1):c.780C>T (p.Pro260=) AND Malignant tumor of breast

Germline classification:
Likely benign (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001354857.2

Allele description [Variation Report for NM_004360.5(CDH1):c.780C>T (p.Pro260=)]

NM_004360.5(CDH1):c.780C>T (p.Pro260=)

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.780C>T (p.Pro260=)
HGVS:
  • NC_000016.10:g.68810289C>T
  • NG_008021.1:g.77998C>T
  • NM_001317184.2:c.780C>T
  • NM_001317185.2:c.-836C>T
  • NM_001317186.2:c.-1040C>T
  • NM_004360.5:c.780C>TMANE SELECT
  • NP_001304113.1:p.Pro260=
  • NP_004351.1:p.Pro260=
  • LRG_301t1:c.780C>T
  • LRG_301:g.77998C>T
  • NC_000016.9:g.68844192C>T
  • NM_004360.3:c.780C>T
  • NM_004360.4:c.780C>T
  • p.P260P
Links:
dbSNP: rs765090311
NCBI 1000 Genomes Browser:
rs765090311
Molecular consequence:
  • NM_001317185.2:c.-836C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1040C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.780C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004360.5:c.780C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Malignant tumor of breast
Synonyms:
Malignant breast neoplasm; Cancer breast
Identifiers:
MONDO: MONDO:0007254; MedGen: C0006142

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001549570Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely benignunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001549570.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The CDH1 p.Pro260= variant was not identified in the literature nor was it identified in the Insight Colon Cancer Gene Variant Database, or Zhejiang Colon Cancer Databases. The variant was identified in the following databases: dbSNP (ID: rs765090311) as With Likely benign allele, ClinVar (classified as likely benign by Ambry Genetics, Invitae, GeneDx), and Clinvitae (classified as likely benign ClinVar, Invitae). The variant was identified in control databases in 7 of 246238 chromosomes at a frequency of 0.00003 increasing the likelihood this could be a low frequency variant (Genome Aggregation Consortium Feb 27, 2017). The p.Pro260= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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

Last Updated: Sep 29, 2024