Genetic Information

Gene & Transcript Details

Gene
ATM
Transcript
NM_000051.3 MANE Select
Total Exons
—
Reference Sequence
NC_000011.9
Alternative Transcripts
IDStatusDetails
NM_000051.3 RefSeq Select 13147 nt | 386–9556
NM_000051.4 MANE Select 12915 nt | 151–9321

Variant Details

HGVS Notation
NM_000051.3:c.1176C>G
Protein Change
G392=
Location
Exon 9 (Exon 9 of )
9
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.492 in 100,000
Extremely Rare
ACMG Criteria Applied BS1

ClinVar

Open
Classification
Likely Benign
3 publications
Publications List
PMID: 20077034

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com.

PMID: 40580951

The frequency of this variant in the general population (http://gnomad.broadinstitute.org) is higher than would generally be expected for pathogenic variants in this gene.

Clinical Statement

"This variant has been reported in ClinVar as Benign (21 clinical laboratories) and as benign (1 clinical laboratories) and as Likely benign (1 clinical laboratories) and as Benign by ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen expert panel."

COSMIC Somatic Evidence

Open
COSMIC ID
Recurrence
0 occurrences
PM1 Criteria
Not Applied
COSMIC Database Preview
COSMIC Preview
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Functional Impact & Domains

Functional Domain

Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain.
Related Variants in This Domain
No evidence of other pathogenic variants at this position in gene ATM.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: ATMG392=ATMG392=SomaticNCBI Gene:472|Show additional gene information Variant OverviewATM, a kinase involved in the DNA damage response, is mutated in various solid and hematologic malignancies.This is a synonymous mutation and is not annotated by OncoKB. JAX-CKB: No results found

Database Previews
OncoKB
OncoKB Preview
JAX-CKB
JAX-CKB Preview

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Computational Analysis

Pathogenicity Predictions

SpliceAI
Predictor Consensus
Mixed/VUS
PP3 Applied
No
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied

SpliceAI Scores

Window: ±500bp
Effect Type Score Position
- Acceptor Loss (AL) 0.37 -110 bp
- Donor Loss (DL) 0.45 59 bp
+ Acceptor Gain (AG) 0.03 120 bp
+ Donor Gain (DG) 0.01 -1 bp
High impact (≥0.5) Medium impact (0.2-0.49) Low impact (<0.2)

VCEP Guidelines

Applied ACMG/AMP Criteria (VCEP Specific)

Filter Criteria:
BP6

BP6 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)