11-108293479-T-C
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_ModeratePM2PP5_Very_Strong
The NM_000051.4(ATM):c.4776+2T>C variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.000000687 in 1,455,110 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_000051.4 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATM | NM_000051.4 | c.4776+2T>C | splice_donor_variant, intron_variant | Intron 31 of 62 | ENST00000675843.1 | NP_000042.3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249594Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135048
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455110Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 724322
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Ataxia-telangiectasia syndrome Pathogenic:7
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The c.4776+2T>C canonical splice donor site variant is predicted to cause abnormal gene splicing. This variant, also known as IVS33+2T>C, has been previously reported in the homozygous and compound heterozygous state in individuals with Ataxia-Telangiectasia (AT) (PMID: 9711876). Functional studies showed that this variant led to in-frame skipping of exon 30, previously referred to as exon 32, and a cell line with this variant in the homozygous state exhibited radiosensitivity (PMID: 9497252, 2491181). Based on the combined evidence, this variant is classified as pathogenic. -
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Variant summary: ATM c.4776+2T>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: Three predict the variant abolishes a 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4.1e-06 in 244642 control chromosomes. c.4776+2T>C has been reported in the literature in at least two individuals affected with Ataxia-Telangiectasia, one of whom is homozygous for the variant with classic A-T with microcephaly and intellectual disability (Gilad_1998). These data indicate that the variant may be associated with disease. Gilad et al. also report experimental evidence suggesting a loss of ATM protein product in the patient's fibroblast cell line, though the data was not presented for review. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and both classified the variant as pathogenic. Furthermore, c.4776+2T>A has also been reported to associate with Ataxia-Telangiectasia. Based on the evidence outlined above, the variant was classified as pathogenic. -
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This sequence change affects a donor splice site in intron 31 of the ATM gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs587781927, gnomAD 0.003%). Disruption of this splice site has been observed in individual(s) with ataxia-telangiectasia (PMID: 9497252, 12815592). 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 IVS33+2T>C. ClinVar contains an entry for this variant (Variation ID: 141672). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that disruption of this splice site affects ATM function (PMID: 2491181, 9497252). Studies have shown that disruption of this splice site results in skipping of exon 31, but is expected to preserve the integrity of the reading-frame (PMID: 9497252; internal data). For these reasons, this variant has been classified as Pathogenic. -
not provided Pathogenic:2
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Canonical splice site variant resulting in skipping of exon 31 (Velazquez 2020); Reported in the homozygous and compound heterozygous state in individuals with ataxia-telangiectasia (Curry 1989, Gilad 1998, Mitui 2003); Functional studies showed a cell line with this variant in the homozygous state exhibited radiosensitivity consistent with classic ataxia-telangiectasia cell lines (Curry 1989, Gilad 1998); Observed in the heterozygous state in an individual with a personal and family history of ATM-related cancers (Velazquez 2020); Not observed at significant frequency in large population cohorts (Lek et al., 2016); Also known as IVS33+2T>C; This variant is associated with the following publications: (PMID: 21445571, 12815592, 15279807, 10330348, 25525159, 9497252, 31019026, 32756499, 2491181) -
Hereditary cancer-predisposing syndrome Pathogenic:2
This variant causes a T to C nucleotide substitution at the +2 position of intron 31 of the ATM gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. RNA studies have shown that this variant leads to the skipping of exon 31, which is expected to result in an in-frame deletion of 55 amino acids (PMID: 9497252, 32756499). Functional studies have shown that the fibroblast cell line derived from a homozygous carrier of this variant exhibits increased radiosensitivity (PMID: 9497252, 2491181). This variant (also known as IVS33+2T>C in the literature) has been reported in the homozygous and compound heterozygous state in individuals affected with ataxia-telangiectasia (PMID: 12815592, 2491181). This variant has also been reported in an individual affected with breast and ovarian cancer (PMID: 32756499). This variant has been identified in 1/249594 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.4776+2T>C intronic pathogenic mutation results from a T to C substitution two nucleotides after coding exon 30 in the ATM gene. This alteration has previously reported in multiple families with ataxia-telangiectasia, and it has been shown to lead to aberrant splicing with no detectable levels of ATM protein production (Mitui M et al. Hum. Mutat. 2003; 22:43-50; Gilad S et al. Am. J. Hum. Genet. 1998; 62:551-61; Teraoka SN et al. Am. J. Hum. Genet. 1999; 64:1617-31). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Of note, this alteration is also designated as IVS33+2T>C in the published literature. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Familial cancer of breast Pathogenic:2
This variant is considered likely 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. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at