NM_000051.4(ATM):c.946T>C (p.Tyr316His) AND not provided

Germline classification:: Conflicting classifications of pathogenicity (2 submissions)
Last evaluated:: Dec 10, 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:: RCV000486900.24

Allele description [Variation Report for NM_000051.4(ATM):c.946T>C (p.Tyr316His)]

NM_000051.4(ATM):c.946T>C (p.Tyr316His)

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.946T>C (p.Tyr316His)

HGVS:

NC_000011.10:g.108247008T>C
NG_009830.1:g.29177T>C
NM_000051.4:c.946T>CMANE SELECT
NM_001351834.2:c.946T>C
NP_000042.3:p.Tyr316His
NP_000042.3:p.Tyr316His
NP_001338763.1:p.Tyr316His
LRG_135t1:c.946T>C
LRG_135:g.29177T>C
LRG_135p1:p.Tyr316His
NC_000011.9:g.108117735T>C
NM_000051.3:c.946T>C

Protein change:

Y316H

Links:

dbSNP: rs142317485

NCBI 1000 Genomes Browser:

rs142317485

Molecular consequence:

NM_000051.4:c.946T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001351834.2:c.946T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000567682	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Dec 10, 2024)	germline	clinical testing	Citation Link,
SCV002821662	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Oct 1, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000567682

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Dec 10, 2024)

germline

clinical testing

Citation Link,

SCV002821662

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Likely benign
(Oct 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, SCV000567682.8

#	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 supports that this missense variant has a deleterious effect on protein structure/function; Observed in individuals with a personal or family history including leukemia and breast cancer as well as in unaffected controls (PMID: 25587027, 27633522, 28779002, 33471991, 34482403); This variant is associated with the following publications: (PMID: 27633522, 25587027, 28779002, 28652578, 30613976, 33471991, 34482403, 37450374, 37529773)

#	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, SCV002821662.15

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

Description

ATM: BP1, BS2

#	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: Jan 19, 2025

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