NM_000051.3(ATM):c.7044G>A (p.Thr2348=) AND Hereditary cancer-predisposing syndrome

Clinical significance:Likely benign (Last evaluated: Feb 14, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000123712.6

Allele description [Variation Report for NM_000051.3(ATM):c.7044G>A (p.Thr2348=)]

NM_000051.3(ATM):c.7044G>A (p.Thr2348=)

Genes:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.3(ATM):c.7044G>A (p.Thr2348=)
Other names:
p.T2348T:ACG>ACA
HGVS:
  • NC_000011.10:g.108327713G>A
  • NG_009830.1:g.109882G>A
  • NG_054724.1:g.147120C>T
  • NM_000051.3:c.7044G>A
  • NM_001330368.2:c.641-18642C>T
  • NM_001351110.2:c.38+7507C>T
  • NM_001351834.2:c.7044G>A
  • NP_000042.3:p.Thr2348=
  • NP_001338763.1:p.Thr2348=
  • LRG_135t1:c.7044G>A
  • LRG_135:g.109882G>A
  • LRG_135p1:p.Thr2348=
  • NC_000011.9:g.108198440G>A
  • p.T2348T
Links:
dbSNP: rs140104789
NCBI 1000 Genomes Browser:
rs140104789
Molecular consequence:
  • NM_001330368.2:c.641-18642C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.38+7507C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000051.3:c.7044G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351834.2:c.7044G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MedGen: C0027672

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000213235Ambry Geneticscriteria provided, single submitter
Likely benign
(Dec 4, 2014)
germlineclinical testing

Citation Link,

SCV000576462Institute for Biomarker Research,Medical Diagnostic Laboratories, L.L.C.criteria provided, single submitter
Likely benign
(Feb 14, 2017)
germlineclinical testing

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

SCV000687753Color Health, Inccriteria provided, single submitter
Likely benign
(May 19, 2016)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not 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 Ambry Genetics, SCV000213235.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

From Institute for Biomarker Research,Medical Diagnostic Laboratories, L.L.C., SCV000576462.1

#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 Color Health, Inc, SCV000687753.1

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

Last Updated: Jun 14, 2021

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