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NM_004360.5(CDH1):c.2628C>T (p.Tyr876=) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Dec 24, 2023
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:
RCV000469536.15

Allele description [Variation Report for NM_004360.5(CDH1):c.2628C>T (p.Tyr876=)]

NM_004360.5(CDH1):c.2628C>T (p.Tyr876=)

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.2628C>T (p.Tyr876=)
HGVS:
  • NC_000016.10:g.68833478C>T
  • NG_008021.1:g.101187C>T
  • NM_001317184.2:c.2445C>T
  • NM_001317185.2:c.1080C>T
  • NM_001317186.2:c.663C>T
  • NM_004360.4:c.2628C>T
  • NM_004360.5:c.2628C>TMANE SELECT
  • NP_001304113.1:p.Tyr815=
  • NP_001304114.1:p.Tyr360=
  • NP_001304115.1:p.Tyr221=
  • NP_004351.1:p.Tyr876=
  • LRG_301t1:c.2628C>T
  • LRG_301:g.101187C>T
  • NC_000016.9:g.68867381C>T
  • NM_004360.3:c.2628C>T
Links:
dbSNP: rs778681919
NCBI 1000 Genomes Browser:
rs778681919
Molecular consequence:
  • NM_001317184.2:c.2445C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001317185.2:c.1080C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001317186.2:c.663C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004360.5:c.2628C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000557391Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Dec 24, 2023)
germlineclinical testing

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

SCV003926969European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de Investigação e Inovação em Saúde, University of Porto - ERN GENTURIS
criteria provided, single submitter

(Lee et al. (Hum Mutat. 2018))
Uncertain significance
(Aug 1, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot provided1not 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

Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline CDH1 sequence variants.

Lee K, Krempely K, Roberts ME, Anderson MJ, Carneiro F, Chao E, Dixon K, Figueiredo J, Ghosh R, Huntsman D, Kaurah P, Kesserwan C, Landrith T, Li S, Mensenkamp AR, Oliveira C, Pardo C, Pesaran T, Richardson M, Slavin TP, Spurdle AB, Trapp M, et al.

Hum Mutat. 2018 Nov;39(11):1553-1568. doi: 10.1002/humu.23650.

PubMed [citation]
PMID:
30311375
PMCID:
PMC6188664
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000557391.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de Investigação e Inovação em Saúde, University of Porto - ERN GENTURIS, SCV003926969.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

"1 family not fulfilling 2020 HDGC criteria-Familial history of breast cancer"

Description

PM2; BP7 (PMID: 30311375)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot provided1not provided

Last Updated: Sep 29, 2024