11-108249096-TG-CT

Variant names:

• chr11-108249096-TG-CT
• NM_000051.4:c.1229_1230delTGinsCT
• ATM p.Val410Ala

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+2 Uncertain · Warm

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_ModerateO7_SupportingB2_Supporting

The NM_000051.4(ATM):c.1229_1230delTGinsCT (p.Val410Ala) variant causes a missense change. The gene ATM is a tumor suppressor gene (CancerMine: 26 TSG, 31 oncogene, 24 driver citations). The gene ATM is a known oncogene (CancerMine: 26 TSG, 31 oncogene, 24 driver citations). The gene ATM is a cancer driver gene (CancerMine: 26 TSG, 31 oncogene, 24 driver citations). Note: allele frequency estimates from gnomAD may be inaccurate for this variant type (MNP or indel longer than 3 bp) due to technology limitations. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.V410A: Conflicting_classifications_of_pathogenicity (ClinVar VariationId 127332); p.V410L: Uncertain_significance (ClinVar VariationId 3967210, 1 star); p.V410M: Conflicting_classifications_of_pathogenicity (ClinVar VariationId 216190); p.V410= (synonymous): Likely_benign (ClinVar VariationId 453357, 2 stars); p.V410= (synonymous): Likely_benign (ClinVar VariationId 1155205, 1 star) This exact variant is curated in the UniProt human variants database as Uncertain Significance; it is also listed as a COSMIC curated somatic variant.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ATM NM_000051.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.12
• Publications: 0 publications found

Genes affected

ATM (HGNC:795): (ATM serine/threonine kinase) The protein encoded by this gene belongs to the PI3/PI4-kinase family. This protein is an important cell cycle checkpoint kinase that phosphorylates; thus, it functions as a regulator of a wide variety of downstream proteins, including tumor suppressor proteins p53 and BRCA1, checkpoint kinase CHK2, checkpoint proteins RAD17 and RAD9, and DNA repair protein NBS1. This protein and the closely related kinase ATR are thought to be master controllers of cell cycle checkpoint signaling pathways that are required for cell response to DNA damage and for genome stability. Mutations in this gene are associated with ataxia telangiectasia, an autosomal recessive disorder. [provided by RefSeq, Aug 2010]

ATM Gene-Disease associations (from GenCC):

• ATM-related cancer predisposition

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• hereditary breast carcinoma

  Inheritance: AD Classification: DEFINITIVE Submitted by: Natera, Ambry Genetics
• ataxia telangiectasia

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Laboratory for Molecular Medicine, ClinGen, G2P, Orphanet, Natera, PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• prostate cancer

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
• sarcoma

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• gastric carcinoma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• hereditary nonpolyposis colon cancer

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

Classification according to ACGS-UK Somatic Oncogenicity v2025

Specifications for ATM are available in the ClinGen Criteria Specification Registry and recommended for reference when assigning criteria.

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])
	O7Mutational hotspot or critical domain		Supporting: cancerhotspots.org hit, critical domain, or missense neighbourhood hotspot; No cancerhotspots.org hit at this position; UniProt domain: 0 pathogenic, 0 benign.; ±8 AA neighbourhood: 3 pathogenic, 3 benign (OR vs. background: 5.0); Variant does not impact splicing — splice-hotspot path not applicable
	B2Does not fit gene mode of action		Activating variant in tumor suppressor gene + same AA change classified germline Benign/Likely Benign — supporting benign evidence (B2, no cancer-type context); Activating variant in tumor suppressor gene + same AA change classified germline Benign/Likely Benign — supporting benign evidence (B2, no cancer-type context)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_000051.4. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	ATM NM_000051.4	MANE Select	c.1229_1230delTGinsCT p.Val410Ala	missense	N/A	Prot: NP_000042.3
	ATM NM_001351834.2		c.1229_1230delTGinsCT p.Val410Ala	missense	N/A	Prot: NP_001338763.1 UniProt:

ATM NM_000051.4

MANE Select

HGVSc / HGVSpc.1229_1230delTGinsCTp.Val410Ala

Exon rankN/A

missense

Prot: NP_000042.3

ATM NM_001351834.2

HGVSc / HGVSpc.1229_1230delTGinsCTp.Val410Ala

Exon rankN/A

missense

Prot: NP_001338763.1UniProt: Q13315

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	ATM ENST00000675843.1	MANE Select	c.1229_1230delTGinsCT p.Val410Ala	missense	N/A	Prot: ENSP00000501606.1 UniProt:
	ATM ENST00000452508.7	TSL:1	c.1229_1230delTGinsCT p.Val410Ala	missense	N/A	Prot: ENSP00000388058.2 UniProt:
	ATM ENST00000531525.3	TSL:1	c.1229_1230delTGinsCT p.Val410Ala	missense	N/A	Prot: ENSP00000434327.3 UniProt:

ATM ENST00000675843.1

MANE Select

HGVSc / HGVSpc.1229_1230delTGinsCTp.Val410Ala

Exon rankN/A

missense

Prot: ENSP00000501606.1UniProt: Q13315

ATM ENST00000452508.7

TSL:1

HGVSc / HGVSpc.1229_1230delTGinsCTp.Val410Ala

Exon rankN/A

missense

Prot: ENSP00000388058.2UniProt: Q13315

ATM ENST00000531525.3

TSL:1

HGVSc / HGVSpc.1229_1230delTGinsCTp.Val410Ala

Exon rankN/A

missense

Prot: ENSP00000434327.3UniProt: H0YDU7

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 2 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 2 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
PhyloP100	Uncertain	7.1

Showing 1 of 1 scores

Splicing Scores

No splicing scores have been computed for this variant.

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

hg19: chr11-108119823;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar