NM_000051.4(ATM):c.3118A>G (p.Met1040Val) AND not provided

Germline classification:: Benign/Likely benign (5 submissions)
Last evaluated:: Oct 13, 2023
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:: RCV000224788.22

Allele description [Variation Report for NM_000051.4(ATM):c.3118A>G (p.Met1040Val)]

NM_000051.4(ATM):c.3118A>G (p.Met1040Val)

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.3118A>G (p.Met1040Val)

Other names:

p.M1040V:ATG>GTG; NM_000051.3(ATM):c.3118A>G; NP_000042.3:p.Met1040Val

HGVS:

NC_000011.10:g.108272572A>G
NG_009830.1:g.54741A>G
NM_000051.4:c.3118A>GMANE SELECT
NM_001351834.2:c.3118A>G
NP_000042.3:p.Met1040Val
NP_000042.3:p.Met1040Val
NP_001338763.1:p.Met1040Val
LRG_135t1:c.3118A>G
LRG_135:g.54741A>G
LRG_135p1:p.Met1040Val
NC_000011.9:g.108143299A>G
NM_000051.3:c.3118A>G
Q13315:p.Met1040Val
p.M1040V

Protein change:

M1040V; MET1040VAL

Links:

UniProtKB: Q13315#VAR_010817; OMIM: 607585.0010; dbSNP: rs3092857

NCBI 1000 Genomes Browser:

rs3092857

Molecular consequence:

NM_000051.4:c.3118A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351834.2:c.3118A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000281553	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Aug 19, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000602561	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Oct 13, 2023)	germline	clinical testing	Citation Link,
SCV000694249	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Jun 6, 2016)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 22529920, 25625042, 9622061, 20305132, 12935933, 17640065, 25480502 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001741410	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV005231014	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Computational refinement of functional single nucleotide polymorphisms associated with ATM gene.

George Priya Doss C, Rajith B.

PLoS One. 2012;7(4):e34573. doi: 10.1371/journal.pone.0034573. Epub 2012 Apr 13.

PubMed [citation]

PMID:: 22529920
PMCID:: PMC3326031

ATM gene mutations in sporadic breast cancer patients from Brazil.

Mangone FR, Miracca EC, Feilotter HE, Mulligan LM, Nagai MA.

Springerplus. 2015;4:23. doi: 10.1186/s40064-015-0787-z.

PubMed [citation]

PMID:: 25625042
PMCID:: PMC4298590

See all PubMed Citations (8)

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000281553.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Converted during submission to Likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.003924	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000602561.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000694249.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

Variant summary: The ATM c.3118A>G (p.Met1040Val) variant involves the alteration of a non-conserved nucleotide. 3/3 in silico tools predict a benign outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 459/122598 control chromosomes (10 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0413846 (428/10342, 10 homozygotes). This frequency is about 10 times the estimated maximal expected allele frequency of a pathogenic ATM variant (0.0039528), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. Variant has been reported by multiple studies in both patients and healthy controls, supporting the non-pathogenic nature of this variant. In addition, multiple clinical diagnostic laboratories classified this variant as benign. Considering the high allele frequency of the variant and the homozygous occurrences in the African subpopulation, it was classified as Benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001741410.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005231014.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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