11-108367112-C-T

Variant names:

• chr11-108367112-C-T
• rs227091
• NM_000051.4:c.*1604C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000051.4(ATM):​c.*1604C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 179,358 control chromosomes in the GnomAD database, including 25,966 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.52 (21735 hom., cov: 32)
  • Exomes 𝑓: 0.56 (4231 hom.)
• Consequence: ATM NM_000051.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.855
• Publications: 21 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]

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 11-108367112-C-T is Benign according to our data. Variant chr11-108367112-C-T is described in ClinVar as Benign. ClinVar VariationId is 302272.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATM	NM_000051.4	c.*1604C>T		3_prime_UTR_variant	Exon 63 of 63	ENST00000675843.1	NP_000042.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATM	ENST00000675843.1	c.*1604C>T		3_prime_UTR_variant	Exon 63 of 63		NM_000051.4	ENSP00000501606.1

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79584 AN: 151850 Hom.: 21724 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.561

GnomAD4 exome AF: 0.555 AC: 15213 AN: 27390 Hom.: 4231 Cov.: 0 AF XY: 0.559 AC XY: 7024 AN XY: 12572

African (AFR) AF: 0.413 AC: 372 AN: 900

American (AMR) AF: 0.578 AC: 356 AN: 616

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 1103 AN: 1730

East Asian (EAS) AF: 0.477 AC: 2635 AN: 5528

South Asian (SAS) AF: 0.636 AC: 154 AN: 242

European-Finnish (FIN) AF: 0.500 AC: 9 AN: 18

Middle Eastern (MID) AF: 0.742 AC: 132 AN: 178

European-Non Finnish (NFE) AF: 0.580 AC: 9249 AN: 15948

Other (OTH) AF: 0.539 AC: 1203 AN: 2230

GnomAD4 genome AF: 0.524 AC: 79618 AN: 151968 Hom.: 21735 Cov.: 32 AF XY: 0.533 AC XY: 39574 AN XY: 74280

African (AFR) AF: 0.371 AC: 15382 AN: 41448

American (AMR) AF: 0.616 AC: 9410 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2221 AN: 3464

East Asian (EAS) AF: 0.435 AC: 2249 AN: 5170

South Asian (SAS) AF: 0.651 AC: 3129 AN: 4806

European-Finnish (FIN) AF: 0.629 AC: 6640 AN: 10554

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.568 AC: 38607 AN: 67952

Other (OTH) AF: 0.562 AC: 1182 AN: 2104

Alfa AF: 0.541 Hom.: 2814

Bravo AF: 0.513

Asia WGS AF: 0.570 AC: 1982 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Ataxia-telangiectasia syndrome Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.94
DANN	Benign	0.75
PhyloP100		-0.85
Mutation Taster		=100/0	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: rs227091; hg19: chr11-108237839;