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NM_004360.5(CDH1):c.1617T>C (p.Thr539=) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jun 11, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002400084.9

Allele description [Variation Report for NM_004360.5(CDH1):c.1617T>C (p.Thr539=)]

NM_004360.5(CDH1):c.1617T>C (p.Thr539=)

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.1617T>C (p.Thr539=)
HGVS:
  • NC_000016.10:g.68819331T>C
  • NG_008021.1:g.87040T>C
  • NM_001317184.2:c.1434T>C
  • NM_001317185.2:c.69T>C
  • NM_001317186.2:c.-254-2670T>C
  • NM_004360.5:c.1617T>CMANE SELECT
  • NP_001304113.1:p.Thr478=
  • NP_001304114.1:p.Thr23=
  • NP_004351.1:p.Thr539=
  • LRG_301t1:c.1617T>C
  • LRG_301:g.87040T>C
  • NC_000016.9:g.68853234T>C
  • NM_004360.3:c.1617T>C
Links:
dbSNP: rs1596960438
NCBI 1000 Genomes Browser:
rs1596960438
Molecular consequence:
  • NM_001317186.2:c.-254-2670T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317184.2:c.1434T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001317185.2:c.69T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004360.5:c.1617T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002708000Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Jun 11, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV002708000.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Nov 3, 2024