NM_004360.5(CDH1):c.48+5_48+6delinsAT AND Hereditary cancer-predisposing syndrome

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: May 28, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV000582474.6

Allele description [Variation Report for NM_004360.5(CDH1):c.48+5_48+6delinsAT]

NM_004360.5(CDH1):c.48+5_48+6delinsAT

Gene:

CDH1:cadherin 1 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_004360.5(CDH1):c.48+5_48+6delinsAT

HGVS:

NC_000016.10:g.68737468_68737469delinsAT
NG_008021.1:g.5177_5178delinsAT
NM_001317184.2:c.48+5_48+6delinsAT
NM_001317185.2:c.-1568+5_-1568+6delinsAT
NM_001317186.2:c.-1772+5_-1772+6delinsAT
NM_004360.5:c.48+5_48+6delinsATMANE SELECT
LRG_301t1:c.48+5_48+6delinsAT
LRG_301:g.5177_5178delinsAT
NC_000016.9:g.68771371_68771372delinsAT
NM_004360.3:c.48+5_48+6delCCinsAT
NM_004360.3:c.48+5_48+6delinsAT
NM_004360.4:c.48+5_48+6delinsAT

Links:

dbSNP: rs1555509656

NCBI 1000 Genomes Browser:

rs1555509656

Molecular consequence:

NM_001317184.2:c.48+5_48+6delinsAT - intron variant - [Sequence Ontology: SO:0001627]
NM_001317185.2:c.-1568+5_-1568+6delinsAT - intron variant - [Sequence Ontology: SO:0001627]
NM_001317186.2:c.-1772+5_-1772+6delinsAT - intron variant - [Sequence Ontology: SO:0001627]
NM_004360.5:c.48+5_48+6delinsAT - intron variant - [Sequence Ontology: SO:0001627]

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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TAFA4 TAFA chemokine like family member 4 [Homo sapiens]
TAFA4 TAFA chemokine like family member 4 [Homo sapiens]
Gene ID:151647

Gene
ATF6B activating transcription factor 6 beta [Macaca mulatta]
ATF6B activating transcription factor 6 beta [Macaca mulatta]
Gene ID:717050

Gene
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000689543	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 28, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002638395	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (May 28, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000689543

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Apr 28, 2017)

germline

clinical testing

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

SCV002638395

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(May 28, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Color Diagnostics, LLC DBA Color Health, SCV000689543.2

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

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

From Ambry Genetics, SCV002638395.2

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

Description

The c.48+5_48+6delCCinsAT intronic variant, located in intron 1 of the CDH1 gene, results from the deletion of two nucleotides and the insertion of two nucleotides five nucleotides after coding exon 1. These nucleotide positions are not well conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration does not have any significant effect on the native donor splice site; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: Sep 29, 2024

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