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NM_004360.5(CDH1):c.147_163+1del AND Hereditary diffuse gastric adenocarcinoma

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 22, 2017
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:
RCV000639207.6

Allele description [Variation Report for NM_004360.5(CDH1):c.147_163+1del]

NM_004360.5(CDH1):c.147_163+1del

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.147_163+1del
HGVS:
  • NC_000016.10:g.68738395_68738412del
  • NG_008021.1:g.6104_6121del
  • NM_001317184.2:c.147_163+1del
  • NM_001317185.2:c.-1469_-1453+1del
  • NM_001317186.2:c.-1673_-1657+1del
  • NM_004360.5:c.147_163+1delMANE SELECT
  • LRG_301t1:c.146_163del
  • LRG_301:g.6104_6121del
  • NC_000016.9:g.68772293_68772310del
  • NC_000016.9:g.68772298_68772315del
  • NM_004360.3:c.146_163delGCCGCGTCCTGGGCAGAG
Links:
dbSNP: rs1555509779
NCBI 1000 Genomes Browser:
rs1555509779
Molecular consequence:
  • NM_001317184.2:c.147_163+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001317185.2:c.-1469_-1453+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001317186.2:c.-1673_-1657+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004360.5:c.147_163+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Hereditary diffuse gastric adenocarcinoma (HDGC)
Synonyms:
Hereditary diffuse gastric cancer
Identifiers:
MONDO: MONDO:0007648; MedGen: C1708349; Orphanet: 26106; OMIM: 137215

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000760776Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 22, 2017) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000760776.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acids is currently unknown. This variant has not been reported in the literature in individuals with CDH1-related disease. This variant is not present in population databases (ExAC no frequency). This variant, c.142_159del, results in the deletion of 6 amino acids of the CDH1 protein (p.Gly49_Arg54del), but otherwise preserves the integrity of the reading frame.

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

Last Updated: Sep 29, 2024