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NM_000051.4(ATM):c.5763-1056G>A AND Familial cancer of breast

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 15, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002266554.8

Allele description [Variation Report for NM_000051.4(ATM):c.5763-1056G>A]

NM_000051.4(ATM):c.5763-1056G>A

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_000051.4(ATM):c.5763-1056G>A
HGVS:
  • NC_000011.10:g.108309104G>A
  • NG_009830.1:g.91273G>A
  • NG_054724.1:g.165729C>T
  • NM_000051.4:c.5763-1056G>AMANE SELECT
  • NM_001330368.2:c.641-33C>T
  • NM_001351110.2:c.*39-33C>T
  • NM_001351834.2:c.5763-1056G>A
  • LRG_135t1:c.5763-1056G>A
  • LRG_135:g.91273G>A
  • NC_000011.9:g.108179831G>A
  • NM_000051.3:c.5763-1056G>A
Links:
dbSNP: rs1325461375
NCBI 1000 Genomes Browser:
rs1325461375
Molecular consequence:
  • NM_000051.4:c.5763-1056G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330368.2:c.641-33C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.*39-33C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351834.2:c.5763-1056G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Familial cancer of breast
Synonyms:
Breast cancer, familial; Hereditary breast cancer
Identifiers:
MONDO: MONDO:0016419; MedGen: C0346153; OMIM: 114480

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002548545Department of Molecular Diagnostics, Institute of Oncology Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(May 15, 2022) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Identification of Spliceogenic Variants beyond Canonical GT-AG Splice Sites in Hereditary Cancer Genes.

Dragoš VŠ, Strojnik K, Klančar G, Škerl P, Stegel V, Blatnik A, Banjac M, Krajc M, Novaković S.

Int J Mol Sci. 2022 Jul 4;23(13). doi:pii: 7446. 10.3390/ijms23137446.

PubMed [citation]
PMID:
35806449
PMCID:
PMC9267136

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 Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SCV002548545.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

ATM:c.5763-1056G>A variant is present in 0.00078% in the large population studies (GnomAd). The deep intronic variant is predicted to strengthen a cryptic donor splice site in intron 38 by in silico splicing tools. Functional RNA study has shown that the variant causes a splicing aberration - pseudoexon inclusion, causing the creation of a premature stop codon (PMID: 35806449). Since it has not been established whether the variant causes complete or incomplete splicing aberration, the variant was classified as variant of uncertain significance (ACMG/AMP: PM2-supp, PP3, PS3-m)

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

Last Updated: Oct 26, 2024