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NM_000051.4(ATM):c.3014A>G (p.Asn1005Ser) AND multiple conditions

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Mar 30, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000515446.6

Allele description [Variation Report for NM_000051.4(ATM):c.3014A>G (p.Asn1005Ser)]

NM_000051.4(ATM):c.3014A>G (p.Asn1005Ser)

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.3014A>G (p.Asn1005Ser)
Other names:
p.N1005S:AAT>AGT
HGVS:
  • NC_000011.10:g.108271343A>G
  • NG_009830.1:g.53512A>G
  • NM_000051.4:c.3014A>GMANE SELECT
  • NM_001351834.2:c.3014A>G
  • NP_000042.3:p.Asn1005Ser
  • NP_000042.3:p.Asn1005Ser
  • NP_001338763.1:p.Asn1005Ser
  • LRG_135t1:c.3014A>G
  • LRG_135:g.53512A>G
  • LRG_135p1:p.Asn1005Ser
  • NC_000011.9:g.108142070A>G
  • NM_000051.3:c.3014A>G
  • p.N1005S
Protein change:
N1005S
Links:
dbSNP: rs146531614
NCBI 1000 Genomes Browser:
rs146531614
Molecular consequence:
  • NM_000051.4:c.3014A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.3014A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Familial cancer of breast
Synonyms:
Breast cancer, familial; Hereditary breast cancer
Identifiers:
MONDO: MONDO:0016419; MedGen: C0346153; OMIM: 114480
Name:
Ataxia-telangiectasia syndrome (AT)
Synonyms:
Louis-Bar syndrome; Cerebello-oculocutaneous telangiectasia; Immunodeficiency with ataxia telangiectasia; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008840; MedGen: C0004135; Orphanet: 100; OMIM: 208900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000611355Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(May 23, 2017) 		unknownclinical testing

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

SCV001468411Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 30, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot 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 Fulgent Genetics, Fulgent Genetics, SCV000611355.1

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

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV001468411.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

ATM NM_000051.3 exon 20 p.Asn1005Ser (c.3014A>G): This variant has been reported in the literature as germline in at least 3 individuals with cancer (Haiman 2013 PMID:23555315, Lu 2015 PMID:26689913, Tung 2016 PMID:26976419). This variant is present in 0.6% (65/10362) of Ashkenazi Jewish alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/11-108142070-A-G?dataset=gnomad_r2_1). This variant is present in ClinVar, with several conflicting interpretations between Variant of Uncertain Significance (VUS) and Likely Benign/Benign (Variation ID:127366). This variant amino acid Serine (Ser) is present in >20 species including mammals and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

Last Updated: Nov 3, 2024