rs587779866
Variant summary
Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1_ModeratePP5_Very_Strong
The NM_000051.4(ATM):c.7630-2A>C variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_000051.4 splice_acceptor, intron
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Pathogenic. The variant received 10 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ATM | NM_000051.4 | c.7630-2A>C | splice_acceptor_variant, intron_variant | Intron 51 of 62 | ENST00000675843.1 | NP_000042.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152152Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00000796 AC: 2AN: 251132 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1460998Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726852 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74328 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Ataxia-telangiectasia syndrome Pathogenic:8
Variant summary: ATM c.7630-2A>C, also known as IVS53-2A>C, is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 3' acceptor site. Three predict the variant strengthens an alternate intronic 3' acceptor site. At least one publication reports experimental evidence that this variant affects mRNA splicing reporting skipping of exon 54 (60%) and skipping of the first 11 nt of exon 54 (40%) (legacy exon numbering) (Sandoval_1999). The variant allele was found at a frequency of 8e-06 in 251132 control chromosomes. c.7630-2A>C has been reported in the literature in multiple individuals affected with Ataxia-Telangiectasia as well as in individuals undergoing multigene panel testing for hereditary cancers (example, Sandoval_1999, Telatar_1998, Susswein_2016, Tsaousis_2019). These data indicate that the variant is very likely to be associated with disease. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic for Ataxia Telangectasia and ATM associated cancers. -
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This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -
This sequence change affects an acceptor splice site in intron 51 of the ATM gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs587779866, gnomAD 0.003%). Disruption of this splice site has been observed in individual(s) with breast cancer and ataxia-telangiectasia (AT) (PMID: 9443866, 9887333, 21833744, 25374739, 26681312). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as IVS51-2A>C and IVS53-2A>C. ClinVar contains an entry for this variant (Variation ID: 127447). Studies have shown that disruption of this splice site results in skipping of exon 52 and activation of a cryptic splice site, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 9887333; internal data). For these reasons, this variant has been classified as Pathogenic. -
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The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.001%). Canonical splice site is predicted to alter splicing and result in a loss or disruption of normal protein function. Multiple pathogenic loss-of-function variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000127447). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
not provided Pathogenic:6
ATM: PS3, PVS1:Strong, PM2, PS4:Moderate -
The c.7630-2A>C sequence change is predicted to abolish the splice acceptor site, and affects splicing of exon 52. RNA study has demonstrated that this variant leads to exon skipping (Sandoval et. al., 1999). This variant has been reported in several patients with ataxia-telangiectasia in the homozygous state or compound heterozygous state with another pathogenic variant (Sandoval et. al., 1999; Podralska et. al., 2014). This variant has also been reported in two patients with breast cancer in the heterozygous state (Susswein et. al., 2016). The contribution of this pathogenic sequence change to this patient's AML remains uncertain. Approximately 10% of patients with ataxia telangiectasia due to biallelic ATM mutations develop cancer, mostly of the lymphoid malignancies including Hodgkin's lymphoma, non-Hodgkin's lymphoma, and several forms of leukemia (Boultwood 2001; Taylor et al., 1996). Heterozygous carriers of pathogenic variants in ATM have been associated with increased risk of breast cancer (Tavtigian et. al., 2009). Our interpretation is based on the current understanding of the genetics of ATM-related diseases. -
Canonical splice site variant demonstrated to cause aberrant splicing by exon skipping or use of a cryptic splice site (Sandoval et al., 1999; Laake et al., 2000); Identified in the homozygous state or with a pathogenic variant on the opposite allele in multiple unrelated patients with ataxia telangiectasia and has been described as a pathogenic founder variant in individuals of Polish descent (Telatar et al., 1998; Li and Swift, 2000; Mitui et al., 2005; Soukupova et al., 2011; Nespoli et al., 2013; Podralska et al., 2014); Observed in the heterozygous state in individuals with ATM-related cancers (Brand et al., 2018; Dudley et al., 2018; Goidescu et al., 2018; Cybulski et al., 2019); Not observed at significant frequency in large population cohorts (gnomAD); Also known as IVS53-2A>C; This variant is associated with the following publications: (PMID: 16411093, 27433846, 28843361, 26580448, 30067863, 31159747, 30772474, 31407689, 25525159, 25374739, 9443866, 25614872, 16266405, 10817650, 21833744, 10980530, 29360161, 15039971, 29785153, 29678143, 30293248, 31173646, 31285527, 34199532, 35716007, 9887333, 10330348) -
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The ATM c.7630-2A>C variant disrupts a canonical splice-acceptor site and interferes with normal ATM mRNA splicing. This variant has been reported in the published literature in the homozygous and compound heterozygous state in individuals affected with Ataxia-Telangiectasia (PMID: 9443866 (1998), 10330348 (1999), 21833744 (2011), 25374739 (2013), 30772474 (2019)). In addition, this variant has been identified in individuals with breast cancer (PMID: 26681312 (2015), 29360161 (2018), 29785153 (2018)), lung cancer (PMID: 28843361 (2017)), and pancreatic cancer (PMID: 30067863 (2018)). A study in cell lines indicated this variant causes exon skipping, and no detectable ATM protein was observed in the homozygous case (PMID: 9887333 (1999)). The frequency of this variant in the general population, 0.000023 (3/128914 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. -
Familial cancer of breast Pathogenic:5
PVS1, PS3_MOD, PM3_VSTR , PM2_SUP -
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This variant is considered pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 9443866, 9887333, 10330348]. Functional studies indicate this variant impacts protein function [PMID: 9443866, 9887333, 10330348]. -
Criteria applied: PVS1,PM3,PM2_SUP -
Hereditary cancer-predisposing syndrome Pathogenic:3
This variant occurs 2 nucleotides before exon 52 of the ATM gene. This position is highly conserved in the human and other genomes and is crucial in mRNA processing. This mutation is expected to result in incorrect splicing, alteration in the reading frame and a truncated protein. This variant is present in population databases ( rs587779866, <0.01%) and the mutation database ClinVar contains an entry for this variant (Variation ID: 127447/). This particular variant has been reported in the literature in individuals affected with ataxia-telangiectasia and in breast cancer patients (PMID: 988733, PMID: 26681312). An experimental study showed that this variant results in two aberrant forms of the ATM transcript, one in which exon 52 is skipped and another in which the first 11 nucleotides of exons 52 are skipped (PMID: 9887333 ). -
This variant causes an A to C nucleotide substitution at the -2 position of intron 51 splice acceptor site of the ATM gene. This variant has been shown to cause aberrant RNA splicing and result in the absence of ATM protein (PMID: 9887333, 35716007). This variant has been reported in multiple individuals affected with breast cancer cancer (PMID: 26681312, 29360161, 33050356) and pancreatic cancer (PMID: 29360161, 30067863; Peters et al., 2017, DOI: 10.1200/JCO.2017.35.15_suppl.1501). This variant has been reported in over ten individuals affected with ataxia-telangiectasia (PMID: 9887333, 10817650, 25374739, 25614872, 30772474, 33330270, 34199532; DOI:10.1016/j.nerep.2021.100011). This variant has been identified in 4/276934 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of ATM function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
The c.7630-2A>C intronic pathogenic mutation results from an A to C substitution two nucleotides upstream from coding exon 51 in the ATM gene. This alteration has been detected in conjunction with another pathogenic mutation in numerous individuals with ataxia telangiectasia and has been shown to result in aberrant splicing and decreased ATM protein levels (Sandoval N et al. Hum. Mol. Genet. 1999 Jan;8:69-79; Teraoka S et al. Am J Hum Genet. 1999 Jun;64(6):1617-31; Coutinho G et al. Am. J. Med. Genet. A. 2004 Apr;126A:33-40; Soukupova J et al. Neuromolecular Med. 2011 Sep;13:204-11; Nespoli L et al. Case Reports Immunol, 2013 Oct;2013:296827; Podralska MJ et al. Mol Genet Genomic Med. 2014 Nov;2:504-11;). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This mutation has also been identified in multiple individuals with breast cancer, metastatic prostate cancer, and pancreatic adenocarcinoma (Susswein LR et al. Genet. Med. 2016 Aug;18:823-32; Pritchard CC et al. N. Engl. J. Med. 2016 Aug;375:443-53; Dudley B et al. Cancer, 2018 Apr;124:1691-1700; Brand R et al. Cancer, 2018 Sep;124:3520-3527). Of note, this alteration is also designated IVS53-2A>C in published literature. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Ataxia-telangiectasia syndrome;C0346153:Familial cancer of breast Pathogenic:1Other:1
Variant interpreted as Pathogenic and reported on 08-13-2018 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -
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Breast and/or ovarian cancer Pathogenic:1
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Colorectal cancer Pathogenic:1
ACMG criteria used to clasify this variant: PVS1, PM2 -
Tip-toe gait Pathogenic:1
Gait disorder -
ATM-related disorder Pathogenic:1
The ATM c.7630-2A>C variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant has been reported with a second ATM variant in many unrelated individuals with ataxia telangiectasia (Sandoval et al. 1999. PubMed ID: 9887333; Mitui et al. 2005. PubMed ID: 16266405; Suspitsin E et al 2019. PubMed ID: 30772474). RT-PCR studies indicate this variant disrupts normal splicing and results in two alternatively spliced products with either skipping of exon 54 or skipping of the first 11 nucleotides of exon 54 (Sandoval et al. 1999. PubMed ID: 9887333). This variant has also been reported in the heterozygous state in individuals with breast cancer (Goidescu et al. 2018. PubMed ID: 29785153; Nurmi et al 2022. PubMed ID: 36551643; Supp. Table S2 Guindalini et al. 2022. PubMed ID: 35264596), pancreatic cancer (Dudley et al 2018. PubMed ID: 29360161; Brand et al 2018. PubMed ID: 30067863), and prostate cancer (Wokołorczyk. 2020. PubMed ID: 32875559). This variant is reported in 0.0023% of alleles in individuals of European (non-Finnish) descent in gnomAD and is interpreted as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/127447). Variants that disrupt the consensus splice acceptor site in ATM are expected to be pathogenic. This variant is interpreted as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at