NM_000051.4(ATM):c.6217C>T (p.Leu2073Phe) AND not specified

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: May 4, 2022
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:: RCV002222447.10

Allele description [Variation Report for NM_000051.4(ATM):c.6217C>T (p.Leu2073Phe)]

NM_000051.4(ATM):c.6217C>T (p.Leu2073Phe)

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.6217C>T (p.Leu2073Phe)

HGVS:

NC_000011.10:g.108317391C>T
NG_009830.1:g.99560C>T
NG_054724.1:g.157442G>A
NM_000051.4:c.6217C>TMANE SELECT
NM_001330368.2:c.641-8320G>A
NM_001351110.2:c.*39-8320G>A
NM_001351834.2:c.6217C>T
NP_000042.3:p.Leu2073Phe
NP_000042.3:p.Leu2073Phe
NP_001338763.1:p.Leu2073Phe
LRG_135t1:c.6217C>T
LRG_135:g.99560C>T
LRG_135p1:p.Leu2073Phe
NC_000011.9:g.108188118C>T
NM_000051.3:c.6217C>T

Protein change:

L2073F

Links:

dbSNP: rs767406075

NCBI 1000 Genomes Browser:

rs767406075

Molecular consequence:

NM_001330368.2:c.641-8320G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*39-8320G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000051.4:c.6217C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001351834.2:c.6217C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002500501	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Mar 19, 2022)	germline	clinical testing	Citation Link,
SCV002517875	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Uncertain significance (May 4, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002500501

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Mar 19, 2022)

germline

clinical testing

Citation Link,

SCV002517875

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2019)

Uncertain significance
(May 4, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002500501.1

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

Description

Variant summary: ATM c.6217C>T (p.Leu2073Phe) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 251372 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.6217C>T in individuals affected with Ataxia-Telangiectasia and no experimental evidence demonstrating its impact on protein function have been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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 Mendelics, SCV002517875.1

#	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

Last Updated: Nov 3, 2024

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