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:
current
Accession:
RCV000587703.5

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

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

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.1953A>G (p.Leu651=)
Other names:
p.L651L:CTA>CTG
HGVS:
  • 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
Links:
dbSNP: rs730881283
NCBI 1000 Genomes Browser:
rs730881283
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]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
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

Citations

PubMed

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]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics,PreventionGenetics, SCV000805510.1

#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 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

Description

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.

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

Last Updated: Dec 4, 2021

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