NM_004360.5(CDH1):c.387+5G>A AND not provided

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: May 11, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000315259.8

Allele description [Variation Report for NM_004360.5(CDH1):c.387+5G>A]

NM_004360.5(CDH1):c.387+5G>A

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.387+5G>A

HGVS:

NC_000016.10:g.68801898G>A
NG_008021.1:g.69607G>A
NM_001317184.2:c.387+5G>A
NM_001317185.2:c.-1229+5G>A
NM_001317186.2:c.-1433+5G>A
NM_004360.5:c.387+5G>AMANE SELECT
LRG_301t1:c.387+5G>A
LRG_301:g.69607G>A
NC_000016.9:g.68835801G>A
NM_004360.3:c.387+5G>A
NM_004360.4:c.387+5G>A
NM_004360.5(CDH1):c.387+5G>AMANE SELECT

Links:

dbSNP: rs113055163

NCBI 1000 Genomes Browser:

rs113055163

Molecular consequence:

NM_001317184.2:c.387+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001317185.2:c.-1229+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001317186.2:c.-1433+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_004360.5:c.387+5G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000329224	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Aug 25, 2020)	germline	clinical testing	Citation Link,
SCV004220830	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Benign (May 11, 2023)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 26123647, 35264596, 31642931, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000329224

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Aug 25, 2020)

germline

clinical testing

Citation Link,

SCV004220830

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Benign
(May 11, 2023)

unknown

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Rare Variants in the Epithelial Cadherin Gene Underlying the Genetic Etiology of Nonsyndromic Cleft Lip with or without Cleft Palate.

Brito LA, Yamamoto GL, Melo S, Malcher C, Ferreira SG, Figueiredo J, Alvizi L, Kobayashi GS, Naslavsky MS, Alonso N, Felix TM, Zatz M, Seruca R, Passos-Bueno MR.

Hum Mutat. 2015 Nov;36(11):1029-33. doi: 10.1002/humu.22827. Epub 2015 Aug 3.

PubMed [citation]

PMID:: 26123647

Detection of germline variants in Brazilian breast cancer patients using multigene panel testing.

Guindalini RSC, Viana DV, Kitajima JPFW, Rocha VM, López RVM, Zheng Y, Freitas É, Monteiro FPM, Valim A, Schlesinger D, Kok F, Olopade OI, Folgueira MAAK.

Sci Rep. 2022 Mar 9;12(1):4190. doi: 10.1038/s41598-022-07383-1.

PubMed [citation]

PMID:: 35264596
PMCID:: PMC8907244

See all PubMed Citations (4)

Details of each submission

From GeneDx, SCV000329224.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Published functional studies demonstrate no damaging effect: no aberrant splicing observed (Karam 2019); Identified in an individual with nonsyndromic cleft lip and palate (Brito 2015); This variant is associated with the following publications: (PMID: 31638429, 31642931, 30661051, 26123647)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004220830.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 25, 2025

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