NM_000051.4(ATM):c.3919G>A (p.Gly1307Arg) AND Malignant tumor of breast

Clinical significance:Likely benign

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001356054.1

Allele description [Variation Report for NM_000051.4(ATM):c.3919G>A (p.Gly1307Arg)]

NM_000051.4(ATM):c.3919G>A (p.Gly1307Arg)

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.3919G>A (p.Gly1307Arg)
HGVS:
  • NC_000011.10:g.108284399G>A
  • NG_009830.1:g.66568G>A
  • NM_000051.4:c.3919G>AMANE SELECT
  • NM_001351834.2:c.3919G>A
  • NP_000042.3:p.Gly1307Arg
  • NP_000042.3:p.Gly1307Arg
  • NP_001338763.1:p.Gly1307Arg
  • LRG_135t1:c.3919G>A
  • LRG_135:g.66568G>A
  • LRG_135p1:p.Gly1307Arg
  • NC_000011.9:g.108155126G>A
  • NM_000051.3:c.3919G>A
  • p.G1307R
Protein change:
G1307R
Links:
dbSNP: rs568451087
NCBI 1000 Genomes Browser:
rs568451087
Molecular consequence:
  • NM_000051.4:c.3919G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.3919G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001551112Department 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

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001551112.1

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

Description

The ATM p.Gly1307Arg variant was not identified in the literature nor was it identified in the GeneInsight-COGR, Cosmic, or MutDB databases. The variant was identified in dbSNP (ID: rs568451087) as "With Likely benign allele", ClinVar (classified as likely benign by Ambry Genetics, Invitae, and GeneDx), and LOVD 3.0 (1x) databases. The variant was identified in control databases in 94 of 276986 chromosomes (2 homozygous) at a frequency of 0.0003 (Genome Aggregation Database Feb 27, 2017). The variant was identified in the following populations: South Asian in 92 of 30782 chromosomes (freq: 0.003), Other in 1 of 6458 chromosomes (freq: 0.0002), and East Asian in 1 of 18852 chromosomes (freq: 0.0001), while the variant was not observed in the African, Latino, European, Ashkenazi Jewish, or Finnish populations. The p.Gly1307 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. 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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