NM_004360.5(CDH1):c.1711+9del AND Hereditary diffuse gastric adenocarcinoma

Germline classification:: Likely benign (1 submission)
Last evaluated:: May 15, 2023
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:: RCV001501024.15

Allele description [Variation Report for NM_004360.5(CDH1):c.1711+9del]

NM_004360.5(CDH1):c.1711+9del

Gene:

CDH1:cadherin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_004360.5(CDH1):c.1711+9del

HGVS:

NC_000016.10:g.68819434del
NG_008021.1:g.87143del
NM_001317184.2:c.1528+9del
NM_001317185.2:c.163+9del
NM_001317186.2:c.-254-2567del
NM_004360.5:c.1711+9delMANE SELECT
LRG_301t1:c.1711+9del
LRG_301:g.87143del
NC_000016.9:g.68853333del
NC_000016.9:g.68853333delG
NC_000016.9:g.68853337del
NM_004360.3:c.1711+9delG

Links:

dbSNP: rs762825233

NCBI 1000 Genomes Browser:

rs762825233

Molecular consequence:

NM_001317184.2:c.1528+9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001317185.2:c.163+9del - intron variant - [Sequence Ontology: SO:0001627]
NM_001317186.2:c.-254-2567del - intron variant - [Sequence Ontology: SO:0001627]
NM_004360.5:c.1711+9del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

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

Recent activity

Clear Turn Off Turn On

Lgi4 leucine-rich repeat LGI family, member 4 [Mus musculus]
Lgi4 leucine-rich repeat LGI family, member 4 [Mus musculus]
Gene ID:243914

Gene
Gentianella amarella internal transcribed spacer 1 (ITS1), specimen voucher NA2 ...
Gentianella amarella internal transcribed spacer 1 (ITS1), specimen voucher NA2 Sullivan
gi|13235133|emb|AJ294591.1|

Nucleotide
Swertia crassiuscula internal transcribed spacer 1 (ITS1)
Swertia crassiuscula internal transcribed spacer 1 (ITS1)
gi|13235534|emb|AJ294637.1|

Nucleotide
Gentianella cernua internal transcribed spacer 2 (ITS2)
Gentianella cernua internal transcribed spacer 2 (ITS2)
gi|13235192|emb|AJ294663.1|

Nucleotide
Swertia macrosperma chloroplast partial matK gene for maturase, exon 1
Swertia macrosperma chloroplast partial matK gene for maturase, exon 1
gi|13235661|emb|AJ406349.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001705828	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (May 15, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001705828

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(May 15, 2023)

germline

clinical testing

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

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

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, SCV001705828.5

#	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

Last Updated: Oct 26, 2024

ClinVar

Relating variation to medicine