rs730882048
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_005431.2(XRCC2):c.96delT(p.Phe32LeufsTer30) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,613,350 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005431.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XRCC2 | NM_005431.2 | c.96delT | p.Phe32LeufsTer30 | frameshift_variant | Exon 2 of 3 | ENST00000359321.2 | NP_005422.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XRCC2 | ENST00000359321.2 | c.96delT | p.Phe32LeufsTer30 | frameshift_variant | Exon 2 of 3 | 1 | NM_005431.2 | ENSP00000352271.1 | ||
XRCC2 | ENST00000495707.1 | n.118delT | non_coding_transcript_exon_variant | Exon 2 of 3 | 1 | |||||
XRCC2 | ENST00000698506.1 | c.-47-11363delT | intron_variant | Intron 1 of 1 | ENSP00000513758.1 | |||||
XRCC2 | ENST00000698507.1 | n.164delT | non_coding_transcript_exon_variant | Exon 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000678 AC: 17AN: 250678Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135540
GnomAD4 exome AF: 0.0000465 AC: 68AN: 1461158Hom.: 0 Cov.: 30 AF XY: 0.0000564 AC XY: 41AN XY: 726834
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74346
ClinVar
Submissions by phenotype
not provided Uncertain:4
Case-control data do not support that this variant is associated with increased risk for breast cancer (Kluzniak 2019); Frameshift variant predicted to result in protein truncation, as the last 249 amino acids are replaced with 29 different amino acids, disrupting the critical Walker A and Walker B ATPase motifs (O'Regan 2001, Miller 2004); Observed in individuals with breast cancer, at least one of whom also harbored a pathogenic ATM variant (Cybulski 2014, Couch 2015, Shirts 2016); Variants in candidate genes are classified as variants of uncertain significance in accordance with ACMG guidelines (Richards et al., 2015); This variant is associated with the following publications: (PMID: 25330149, 26689913, 25452441, 26681312, 26845104, 30322717, 31463769) -
The XRCC2 c.96del (p.Phe32Leufs*30) variant alters the translational reading frame of the XRCC2 mRNA and is predicted to cause the premature termination of XRCC2 protein synthesis. This variant is not expected to trigger nonsense mediated decay (NMD), however ~89% of the protein is disrupted, and thus predicted to significantly impact protein function. In the published literature, this variant has been reported in individuals with breast cancer (PMID: 39003306 (2024), 36290365 (2022), 31463769 (2019), 31173646 (2019), 25452441 (2015), 26681312 (2015), 25330149 (2015)), ovarian cancer (PMID: 36290365 (2022), 30322717 (2018), 29053726 (2017)), melanoma (PMID: 29641532 (2018)), and gastric cancer (PMID: 36290365 (2022)). This variant has also been identified in reportedly healthy individuals (PMID: 31463769 (2019), 29641532 (2018)). The frequency of this variant in the general population, 0.00015 (19/128916 chromosomes in European (Non-Finnish) subpopulation (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is higher than would generally be expected for pathogenic variants in this gene. Based on the available information, we are unable to determine the clinical significance of this variant. -
This sequence change creates a premature translational stop signal (p.Phe32Leufs*30) in the XRCC2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 249 amino acid(s) of the XRCC2 protein. This variant is present in population databases (rs730882048, gnomAD 0.02%). This premature translational stop signal has been observed in individual(s) with breast cancer and ovarian cancer (PMID: 25330149, 25452441, 26681312, 26845104, 30322717, 31463769, 35988656). This variant is also known as c.95delT. ClinVar contains an entry for this variant (Variation ID: 183003). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
XRCC2: PVS1:Strong -
Hereditary cancer-predisposing syndrome Pathogenic:1Uncertain:1
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The c.96delT variant, located in coding exon 2 of the XRCC2 gene, results from a deletion of one nucleotide at nucleotide position 96, causing a translational frameshift with a predicted alternate stop codon (p.F32Lfs*30). The predicted stop codon occurs in the 5’ end of theXRCC2 gene. Premature termination codons in the 5’ end of a gene have been reported to escape nonsense-mediated mRNAdecay and/or lead to re-initiation (Rivas et al. Science. 2015 May 8;348(6235):666-9; Lindeboom et al. Nat Genet. 2016 Oct;48(10):1112-8; Rhee et al. Sci Rep. 2017 May 10;7(1):1653). Direct evidence for this alteration is unavailable, however premature termination codons are typically deleterious in nature. This alteration has been identified in multiple individuals diagnosed with breast and/or ovarian cancer (Couch FJ et al. J. Clin. Oncol. 2015 Feb;33:304-11; Cybulski C et al. Clin. Genet. 2015 Oct;88:366-70; Shirts BH et al. Genet. Med. 2016 Oct;18:974-81; Carter NJ et al. Gynecol Oncol. 2018 12;151:481-488). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
Breast carcinoma Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at