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NM_000051.4(ATM):c.3754T>C (p.Tyr1252His) AND Malignant tumor of breast

Germline classification:
Uncertain significance (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001355826.2

Allele description [Variation Report for NM_000051.4(ATM):c.3754T>C (p.Tyr1252His)]

NM_000051.4(ATM):c.3754T>C (p.Tyr1252His)

Gene:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.3754T>C (p.Tyr1252His)
HGVS:
  • NC_000011.10:g.108284234T>C
  • NG_009830.1:g.66403T>C
  • NM_000051.4:c.3754T>CMANE SELECT
  • NM_001351834.2:c.3754T>C
  • NP_000042.3:p.Tyr1252His
  • NP_001338763.1:p.Tyr1252His
  • LRG_135:g.66403T>C
  • NC_000011.9:g.108154961T>C
Protein change:
Y1252H
Links:
dbSNP: rs2135704307
NCBI 1000 Genomes Browser:
rs2135704307
Molecular consequence:
  • NM_000051.4:c.3754T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.3754T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Malignant tumor of breast
Synonyms:
Malignant breast neoplasm; Cancer breast
Identifiers:
MONDO: MONDO:0007254; MedGen: C0006142

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001550825Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Uncertain significanceunknownclinical testing

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes0not providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001550825.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided0not providednot providedclinical testingnot provided

Description

The ATM p.Tyr1252His variant was not identified in the literature nor was it identified in the dbSNP, ClinVar, Cosmic, MutDB, LOVD 3.0, databases. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Tyr1252His residue is conserved in mammals but not in more distantly related organisms however four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided0not providednot providednot provided

Last Updated: Dec 24, 2023