NM_000051.4(ATM):c.7886_7890del (p.Ile2629fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Mar 23, 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:: RCV000483952.29

Allele description [Variation Report for NM_000051.4(ATM):c.7886_7890del (p.Ile2629fs)]

NM_000051.4(ATM):c.7886_7890del (p.Ile2629fs)

Genes:

ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.7886_7890del (p.Ile2629fs)

Other names:

7883del5

HGVS:

NC_000011.10:g.108332854TATTA[1]
NG_009830.1:g.115023TATTA[1]
NG_054724.1:g.141973TATAA[1]
NM_000051.4:c.7886_7890delMANE SELECT
NM_001330368.2:c.641-23784_641-23780del
NM_001351110.2:c.*38+2365_*38+2369del
NM_001351834.2:c.7886_7890del
NP_000042.3:p.Ile2629Serfs
NP_000042.3:p.Ile2629fs
NP_001338763.1:p.Ile2629fs
LRG_135t1:c.7881_7885TATTA[1]
LRG_135:g.115023TATTA[1]
LRG_135p1:p.Ile2629Serfs
NC_000011.9:g.108203578_108203582del
NC_000011.9:g.108203581TATTA[1]
NM_000051.3:c.7881_7885TATTA[1]
NM_000051.3:c.7883_7887delTTATA
NM_000051.3:c.7886_7890del
NM_000051.3:c.7886_7890del
NM_000051.3:c.7886_7890delTATTA
NP_000042.3:p.Ile2629SerfsTer25
c.7883_7887del5

Protein change:

I2629fs

Links:

OMIM: 607585.0015; dbSNP: rs1450394308

NCBI 1000 Genomes Browser:

rs1450394308

Molecular consequence:

NM_000051.4:c.7886_7890del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001351834.2:c.7886_7890del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330368.2:c.641-23784_641-23780del - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+2365_*38+2369del - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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transcription elongation factor A protein-like 4 isoform 1 [Homo sapiens]
transcription elongation factor A protein-like 4 isoform 1 [Homo sapiens]
gi|65505873|ref|NP_079139.4|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000568334	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 23, 2022)	germline	clinical testing	Citation Link,
SCV002063009	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Dec 1, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000568334

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 23, 2022)

germline

clinical testing

Citation Link,

SCV002063009

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Pathogenic
(Dec 1, 2021)

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, SCV000568334.5

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Observed in individuals with a personal or family history consistent with pathogenic variants in this gene referred for genetic testing at GeneDx and in published literature (Goldgar 2011, Hirotsu 2015, Momozawa 2018, Kaneyasu 2020); Not observed at significant frequency in large population cohorts (gnomAD); Also known as c.7883del5, c.7884_7888del5, c.7886_7889del5, and c.7878_7882del; This variant is associated with the following publications: (PMID: 8845835, 21459046, 21787400, 23946315, 9463314, 20346647, 9711876, 26436112, 9443866, 34489640, 29360550, 30287823, 32566746, 34262154, 9600235, 23322442, 12815592)

#	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, SCV002063009.20

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

Last Updated: Nov 10, 2024

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