chr11-108233798-A-G

Variant names:

• chr11-108233798-A-G
• rs228594
• NM_000051.4:c.332-1872A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000051.4(ATM):​c.332-1872A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,638 control chromosomes in the GnomAD database, including 28,594 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (28594 hom., cov: 29)
• Consequence: ATM NM_000051.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 5 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):

• hereditary breast carcinoma

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

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

  Inheritance: AD Classification: MODERATE, LIMITED Submitted by: ClinGen, Ambry Genetics
• prostate cancer

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

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• familial ovarian cancer

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• gastric carcinoma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

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

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATM	NM_000051.4	MANE Select	c.332-1872A>G		intron	N/A	NP_000042.3
	ATM	NM_001351834.2		c.332-1872A>G		intron	N/A	NP_001338763.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATM	ENST00000675843.1	MANE Select	c.332-1872A>G		intron	N/A	ENSP00000501606.1
	ATM	ENST00000452508.7	TSL:1	c.332-1872A>G		intron	N/A	ENSP00000388058.2
	ATM	ENST00000531525.3	TSL:1	c.332-1872A>G		intron	N/A	ENSP00000434327.3

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92672 AN: 151520 Hom.: 28566 Cov.: 29

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.623

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.612 AC: 92740 AN: 151638 Hom.: 28594 Cov.: 29 AF XY: 0.616 AC XY: 45652 AN XY: 74068

African (AFR) AF: 0.654 AC: 27014 AN: 41296

American (AMR) AF: 0.658 AC: 10019 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2324 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2304 AN: 5140

South Asian (SAS) AF: 0.653 AC: 3146 AN: 4820

European-Finnish (FIN) AF: 0.631 AC: 6613 AN: 10484

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39201 AN: 67896

Other (OTH) AF: 0.623 AC: 1308 AN: 2098

Alfa AF: 0.596 Hom.: 3508

Bravo AF: 0.612

Asia WGS AF: 0.597 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		-0.50
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs228594; hg19: chr11-108104525;