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NM_000051.4(ATM):c.1986T>C (p.Phe662=) AND Malignant tumor of breast

Germline classification:
Likely benign (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:
RCV001356414.10

Allele description [Variation Report for NM_000051.4(ATM):c.1986T>C (p.Phe662=)]

NM_000051.4(ATM):c.1986T>C (p.Phe662=)

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.1986T>C (p.Phe662=)
Other names:
p.F662F:TTT>TTC
HGVS:
  • NC_000011.10:g.108253901T>C
  • NG_009830.1:g.36070T>C
  • NM_000051.4:c.1986T>CMANE SELECT
  • NM_001351834.2:c.1986T>C
  • NP_000042.3:p.Phe662=
  • NP_000042.3:p.Phe662=
  • NP_001338763.1:p.Phe662=
  • LRG_135t1:c.1986T>C
  • LRG_135:g.36070T>C
  • LRG_135p1:p.Phe662=
  • NC_000011.9:g.108124628T>C
  • NM_000051.3:c.1986T>C
  • p.F662F
  • p.Phe662Phe
Links:
dbSNP: rs1800055
NCBI 1000 Genomes Browser:
rs1800055
Molecular consequence:
  • NM_000051.4:c.1986T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351834.2:c.1986T>C - synonymous variant - [Sequence Ontology: SO:0001819]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001551576Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely benignunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot 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), SCV001551576.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The ATM p.Phe662= variant was identified in 2 of 348 proband chromosomes (frequency: 0.006) from Swedish and Canadian individuals or families with breast cancer (and a family history of tumours associated with AT) and non-Hodgkin lymphoma, and was not identified in 126 control chromosomes from healthy individuals (Vorechovsky_1996_ 8797579, Sipahimalani_2007_17640065). The variant was also found in 2 cell lines derived from non-lymphoid malignancies (Ejima_2000_ 10738255). The variant was identified in dbSNP (ID: rs1800055) “With Likely benign allele”, ClinVar (classified benign by GeneDx, and likely benign by Invitae, Ambry Genetics, Color Genomics Inc and ARUP), Clinvitae (3x), and was not identified in Cosmic, MutDB, LOVD 3.0, or ATM-LOVD. The variant was also identified in control databases in 133 of 277116 chromosomes at a frequency of 0.0005 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Observation by population include: African in 2 of 24036 chromosomes (freq: 0.00008), “Other” in 3 of 6460 chromosomes (freq: 0.0005), Latino in 10 of 34418 chromosomes (freq: 0.0003), European Non-Finnish in 105 of 126626 chromosomes (freq: 0.0008), Ashkenazi Jewish in 11 of 10148 chromosomes (freq: 0.001), and European Finnish in 2 of 25782 chromosomes (freq: 0.00008); it was not observed in the East Asian and South Asian populations. The p.Phe662= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, 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 although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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

Last Updated: Jan 19, 2025