NM_000051.4(ATM):c.7808A>G (p.Asn2603Ser) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Aug 28, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV003325466.16

Allele description [Variation Report for NM_000051.4(ATM):c.7808A>G (p.Asn2603Ser)]

NM_000051.4(ATM):c.7808A>G (p.Asn2603Ser)

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.7808A>G (p.Asn2603Ser)

HGVS:

NC_000011.10:g.108332781A>G
NG_009830.1:g.114950A>G
NG_054724.1:g.142052T>C
NM_000051.4:c.7808A>GMANE SELECT
NM_001330368.2:c.641-23710T>C
NM_001351110.2:c.*38+2439T>C
NM_001351834.2:c.7808A>G
NP_000042.3:p.Asn2603Ser
NP_000042.3:p.Asn2603Ser
NP_001338763.1:p.Asn2603Ser
LRG_135t1:c.7808A>G
LRG_135:g.114950A>G
LRG_135p1:p.Asn2603Ser
NC_000011.9:g.108203508A>G
NM_000051.3:c.7808A>G

Protein change:

N2603S

Links:

dbSNP: rs150355232

NCBI 1000 Genomes Browser:

rs150355232

Molecular consequence:

NM_001330368.2:c.641-23710T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+2439T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000051.4:c.7808A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351834.2:c.7808A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV004031772	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Aug 28, 2024)	germline	clinical testing	Citation Link,
SCV004133275	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Apr 1, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004031772

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Aug 28, 2024)

germline

clinical testing

Citation Link,

SCV004133275

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Apr 1, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV004031772.2

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; Observed in an individual with colon cancer (PMID: 29684080); This variant is associated with the following publications: (PMID: 29684080)

#	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 CeGaT Center for Human Genetics Tuebingen, SCV004133275.9

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

Description

ATM: BP4

#	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		1	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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