11-108332040-A-G

Variant names:

• chr11-108332040-A-G
• rs869312788
• NM_000051.4:c.7788+3A>G

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2 PP3_Strong PP5

The NM_000051.4(ATM):​c.7788+3A>G variant causes a splice region, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ATM NM_000051.4 splice_region, intron
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:1
• Conservation: PhyloP100: 4.63

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

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 11-108332040-A-G is Pathogenic according to our data. Variant chr11-108332040-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 420257.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, Uncertain_significance=1, Pathogenic=2}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATM	NM_000051.4	c.7788+3A>G		splice_region_variant, intron_variant	Intron 52 of 62	ENST00000675843.1	NP_000042.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATM	ENST00000675843.1	c.7788+3A>G		splice_region_variant, intron_variant	Intron 52 of 62		NM_000051.4	ENSP00000501606.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Ataxia-telangiectasia syndrome Pathogenic:2

Dec 17, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: ATM c.7788+3A>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: One predicts the variant weakens a 5' donor site. One predicts the variant abolishes a 5' splicing donor site. Functional studies report that the variant resulted in aberrant splicing (PMID: 33011440, Internal data). The variant was absent in 250802 control chromosomes (gnomAD). c.7788+3A>G has been reported in the literature in at least an individual affected with Ataxia-Telangiectasia where it was seen in trans with a pathogenic variant (DeStefano_2016). The following publications have been ascertained in the context of this evaluation (PMID: 26845104, 33011440). ClinVar contains an entry for this variant (Variation ID: 420257). Based on the evidence outlined above, the variant was classified as pathogenic. -

Apr 05, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 52 of the ATM gene. It does not directly change the encoded amino acid sequence of the ATM protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with ataxia-telangiectasia and/or breast cancer (PMID: 33011440; De Stefano et al. 2016. J Lab Med. 40(4): 255–261). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 420257). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 52, but is expected to preserve the integrity of the reading-frame (PMID: 33011440; Invitae). This variant disrupts a region of the ATM protein in which other variant(s) (p.Arg2547_Ser2549del) have been determined to be pathogenic (PMID: 7792600, 8797579, 11382771, 12552559, 21787400, 22649200). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1 Uncertain:1

Oct 06, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.7788+3A>G intronic variant results from an A to G substitution 3 nucleotides after coding exon 51 in the ATM gene. This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. In a study involving RNA extraction for RT-PCR and Sanger sequencing of 10 hereditary cancer genes, incomplete disruption of the natural splice site was observed for this alteration (Rofes P et al. J Mol Diagn, 2020 12;22:1453-1468). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Jun 17, 2020

Spanish ATM Cancer Susceptibility Variant Interpretation Working Group

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.7788+3A>G variant it is predicted to disrupt the donor splice site for intron 52. The skipping of exon 52 predicted by default would result in an in-frame deletion of 53 codons (r. .7630_7788del, p.Leu2544_Glu2596del, PP3). Splicing studies performed by two independent laboratories with heterozygous carrier RNA from breast cancer patients confirmed the presence of the predicted transcript with a band intensity comparable to that of the wild-type band (r.7630_7927del p.Leu2544Lysfs*3, O. Díez, unpublished and PMID: 33011440). Sanger sequencing also revealed a very minor transcript corresponding to the out-of-frame skipping of exons 52 and 53 (PMID: 33011440). Although the major transcript is in frame, the skipped exon 52 is located in the FAT domain and contains the nucleotides deleted in the pathogenic in-frame deletion pathogenic variant c.7638_7646del. These RNA results and their expected consequence allow for a funtional supporting code (PS3_Supporting). The c.7788+3A>G variant is absent from the gnomAD v2.1.1 non-cancer dataset, in a position with adequate coverage (>20x) (PM2; http://gnomad.broadinstitute.org). It has been reported in one ataxia-telangiectasia proband in trans with c.5932G > T (p.Glu1978*), which awards it with 1 point as per ClinGen SVI Recommendation for in trans Criterion (PM3, De Stefano, 2016 https://doi.org/10.1515/labmed-2016-0018). Therefore, this variant meets criteria to be classified as pathogenic. Adapted ACMG/AMP rules applied as defined by the Spanish ATM working group: PM2 + PM3 + PP3 + PS3_Supporting (PMID: 33280026). -

not provided Pathogenic:1

Feb 01, 2023

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Intronic variant demonstrated to result in the in-frame skipping of exon 52, which includes the critical FAT domain, as well as out-of-frame exons 52-53, and exon 53 (Stracker et al., 2014; Rofes et al., 2020); Non-canonical splice site variant expected to result in aberrant splicing; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 33011440, 33280026, 23532176, DeStefano2016[Article]) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Uncertain	24
DANN	Benign	0.95

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.96
SpliceAI score (max)		0.76		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.76		Position offset: -3

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

Publications

LitVar

Other links and lift over

dbSNP: rs869312788; hg19: chr11-108202767;