NM_000051.4(ATM):c.1953A>G (p.Leu651=) AND not provided

Clinical significance:Likely benign (Last evaluated: Jan 30, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_000051.4(ATM):c.1953A>G (p.Leu651=)]

NM_000051.4(ATM):c.1953A>G (p.Leu651=)

ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000051.4(ATM):c.1953A>G (p.Leu651=)
Other names:
  • NC_000011.10:g.108253868A>G
  • NG_009830.1:g.36037A>G
  • NM_000051.4:c.1953A>GMANE SELECT
  • NM_001351834.2:c.1953A>G
  • NP_000042.3:p.Leu651=
  • NP_000042.3:p.Leu651=
  • NP_001338763.1:p.Leu651=
  • LRG_135t1:c.1953A>G
  • LRG_135:g.36037A>G
  • LRG_135p1:p.Leu651=
  • NC_000011.9:g.108124595A>G
  • NM_000051.3:c.1953A>G
  • p.L651L
dbSNP: rs730881283
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000051.4:c.1953A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351834.2:c.1953A>G - synonymous variant - [Sequence Ontology: SO:0001819]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000805510PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Likely benign
(Jan 30, 2017)
germlineclinical testing

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

SCV001551243Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedLikely benignunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing



Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

Details of each submission

From PreventionGenetics,PreventionGenetics, SCV000805510.1

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

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001551243.1

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


The ATM p.Leu651= variant was identified in 14 of 14208 proband chromosomes (frequency: 0.001) from Japanese individuals or families with breast cancer and was present in 43 of 47462 control chromosomes (frequency: 0.0009) from healthy individuals (Momozawa 2018). The variant was also identified in dbSNP (ID: rs730881283) “With Uncertain significance allele”, ClinVar (classified as benign by GeneDx; as likely benign by Ambry Genetics, Invitae, Color, and Prevention Genetics; and as uncertain significance by Integrated Genetics/Laboratory Corporation of America), and LOVD 3.0 (1x as benign). The variant was identified in control databases in 22 of 277048 chromosomes at a frequency of 0.00008 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 1 of 24030 chromosomes (freq: 0.00004), Other in 1 of 6460 chromosomes (freq: 0.0002), Latino in 14 of 34416 chromosomes (freq: 0.0004), European Non-Finnish in 5 of 126592 chromosomes (freq: 0.00004), and South Asian in 1 of 30778 chromosomes (freq: 0.00003), while not observed in the Ashkenazi Jewish, East Asian, or European Finnish populations. The p.Leu651= 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) 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.

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

Last Updated: Dec 4, 2021

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