rs3092993

Variant names:

• chr11-108364388-C-A
• rs3092993
• NM_000051.4:c.8851-694C>A

Variant summary

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

The NM_000051.4(ATM):​c.8851-694C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,126 control chromosomes in the GnomAD database, including 1,205 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 0.11 (1205 hom., cov: 32)
• Consequence: ATM NM_000051.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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]

C11orf65 (HGNC:28519): (chromosome 11 open reading frame 65) Predicted to be involved in negative regulation of mitochondrial fission and negative regulation of protein targeting to mitochondrion. Predicted to be located in cytosol and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATM	NM_000051.4	c.8851-694C>A		intron_variant	Intron 61 of 62	ENST00000675843.1	NP_000042.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATM	ENST00000675843.1	c.8851-694C>A		intron_variant	Intron 61 of 62		NM_000051.4	ENSP00000501606.1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16164 AN: 152008 Hom.: 1205 Cov.: 32

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.0910

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.00791

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.106 AC: 16167 AN: 152126 Hom.: 1205 Cov.: 32 AF XY: 0.108 AC XY: 8064 AN XY: 74338

Gnomad4 AFR AF: 0.0239 AC: 0.0239334 AN: 0.0239334

Gnomad4 AMR AF: 0.0909 AC: 0.0908675 AN: 0.0908675

Gnomad4 ASJ AF: 0.144 AC: 0.144175 AN: 0.144175

Gnomad4 EAS AF: 0.00793 AC: 0.00793037 AN: 0.00793037

Gnomad4 SAS AF: 0.0742 AC: 0.0742431 AN: 0.0742431

Gnomad4 FIN AF: 0.238 AC: 0.237851 AN: 0.237851

Gnomad4 NFE AF: 0.145 AC: 0.144645 AN: 0.144645

Gnomad4 OTH AF: 0.103 AC: 0.10322 AN: 0.10322

Alfa AF: 0.118 Hom.: 201

Bravo AF: 0.0927

Asia WGS AF: 0.0370 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.57
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

Publications

LitVar

Other links and lift over

dbSNP: rs3092993; hg19: chr11-108235115;