NM_000051.4(ATM):c.7789-3_7789-2delinsAT AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 20, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV004508401.1

Allele description [Variation Report for NM_000051.4(ATM):c.7789-3_7789-2delinsAT]

NM_000051.4(ATM):c.7789-3_7789-2delinsAT

Genes:

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

Variant type:

Indel

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.7789-3_7789-2delinsAT

HGVS:

NC_000011.10:g.108332759_108332760delinsAT
NG_009830.1:g.114928_114929delinsAT
NG_054724.1:g.142073_142074delinsAT
NM_000051.4:c.7789-3_7789-2delinsATMANE SELECT
NM_001330368.2:c.641-23689_641-23688delinsAT
NM_001351110.2:c.*38+2460_*38+2461delinsAT
NM_001351834.2:c.7789-3_7789-2delinsAT
LRG_135t1:c.7789-3_7789-2delTAinsAT
LRG_135:g.114928_114929delinsAT
NC_000011.9:g.108203486_108203487delinsAT
NM_000051.3:c.7789-3_7789-2delTAinsAT

Molecular consequence:

NM_001330368.2:c.641-23689_641-23688delinsAT - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+2460_*38+2461delinsAT - intron variant - [Sequence Ontology: SO:0001627]
NM_000051.4:c.7789-3_7789-2delinsAT - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001351834.2:c.7789-3_7789-2delinsAT - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

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Homo sapiens calbindin 1 (CALB1), transcript variant 1, mRNA
Homo sapiens calbindin 1 (CALB1), transcript variant 1, mRNA
gi|746815960|ref|NM_004929.3|

Nucleotide
Mus musculus G protein-coupled receptor 157 (Gpr157), mRNA
Mus musculus G protein-coupled receptor 157 (Gpr157), mRNA
gi|110815862|ref|NM_177366.3|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005020142	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely pathogenic (Dec 20, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005020142

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely pathogenic
(Dec 20, 2023)

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 Ambry Genetics, SCV005020142.1

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

Description

The c.7789-3_7789-2delTAinsAT intronic variant results from a deletion of 2 nucleotides and insertion of 2 nucleotides at positions c..7789-3 to c.77889-2 and involves the canonical splice acceptor site before coding exon 52 of the ATM gene. The canonical splice acceptor site is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site; however, direct evidence is insufficient at this time (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.

#	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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