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NM_004360.5(CDH1):c.304G>A (p.Ala102Thr) AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Benign (1 submission)
Last evaluated:
Aug 10, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV003328228.4

Allele description [Variation Report for NM_004360.5(CDH1):c.304G>A (p.Ala102Thr)]

NM_004360.5(CDH1):c.304G>A (p.Ala102Thr)

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.304G>A (p.Ala102Thr)
Other names:
p.A102T:GCC>ACC
HGVS:
  • NC_000016.10:g.68801810G>A
  • NG_008021.1:g.69519G>A
  • NM_001317184.2:c.304G>A
  • NM_001317185.2:c.-1312G>A
  • NM_001317186.2:c.-1516G>A
  • NM_004360.5:c.304G>AMANE SELECT
  • NP_001304113.1:p.Ala102Thr
  • NP_004351.1:p.Ala102Thr
  • LRG_301t1:c.304G>A
  • LRG_301:g.69519G>A
  • NC_000016.9:g.68835713G>A
  • NM_004360.3:c.304G>A
  • NM_004360.4:c.304G>A
  • NM_004360.5(CDH1):c.304G>AMANE SELECT
  • p.A102T
  • p.Ala102Thr
Protein change:
A102T
Links:
dbSNP: rs368492235
NCBI 1000 Genomes Browser:
rs368492235
Molecular consequence:
  • NM_001317185.2:c.-1312G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1516G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.304G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.304G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
CDH1-related diffuse gastric and lobular breast cancer syndrome
Synonyms:
CDH1-related diffuse gastric and lobular breast cancer
Identifiers:
MONDO: MONDO:0100488; MedGen: CN311521

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001142223ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Benign
(Aug 10, 2023) 		germlinecuration

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

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Detection of high frequency of mutations in a breast and/or ovarian cancer cohort: implications of embracing a multi-gene panel in molecular diagnosis in India.

Mannan AU, Singh J, Lakshmikeshava R, Thota N, Singh S, Sowmya TS, Mishra A, Sinha A, Deshwal S, Soni MR, Chandrasekar A, Ramesh B, Ramamurthy B, Padhi S, Manek P, Ramalingam R, Kapoor S, Ghosh M, Sankaran S, Ghosh A, Veeramachaneni V, Ramamoorthy P, et al.

J Hum Genet. 2016 Jun;61(6):515-22. doi: 10.1038/jhg.2016.4. Epub 2016 Feb 25.

PubMed [citation]
PMID:
26911350

Details of each submission

From ClinGen CDH1 Variant Curation Expert Panel, SCV001142223.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

The c.304G>A variant has an allele frequency of 0.00188 (0.19%, 58/30,780 alleles) in the South Asian subpopulation of the gnomAD 2.1.1 cohort (BS1; http://gnomad.broadinstitute.org). The variant was observed in the homozygous state in gnomAD 2.1.1 (BP2). The variant has also been observed in >10 individuals without a diagnosis of diffuse gastric cancer, signet ring tumor or lobular breast cancer and whose family histories do not suggest HDGC (BS2; SCV000210895.12; SCV000186827.5). Therefore, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BS1, BS2, BP2 .

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

Last Updated: Oct 13, 2024