rs201120953
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The ENST00000378823.8(RAD50):āc.1663A>Gā(p.Ile555Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000485 in 1,608,408 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I555K) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000378823.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAD50 | NM_005732.4 | c.1663A>G | p.Ile555Val | missense_variant | 11/25 | ENST00000378823.8 | NP_005723.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAD50 | ENST00000378823.8 | c.1663A>G | p.Ile555Val | missense_variant | 11/25 | 1 | NM_005732.4 | ENSP00000368100 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000798 AC: 20AN: 250738Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135620
GnomAD4 exome AF: 0.0000460 AC: 67AN: 1456296Hom.: 0 Cov.: 31 AF XY: 0.0000552 AC XY: 40AN XY: 724806
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74308
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 08, 2023 | The p.I555V variant (also known as c.1663A>G), located in coding exon 11 of the RAD50 gene, results from an A to G substitution at nucleotide position 1663. The isoleucine at codon 555 is replaced by valine, an amino acid with highly similar properties. This variant was reported in 2/96 patients with pancreatic ductal adenocarcinoma, unselected for family history, who underwent a 22 gene panel test (Hu C et al. Cancer Epidemiol. Biomarkers Prev. 2016 Jan;25:207-11). This variant has also been reported in multiple breast cancer cohorts (Goidescu IG et al. Clujul Med, 2018 Apr;91:157-165; Tsaousis GN et al. BMC Cancer, 2019 Jun;19:535; Akcay IM et al. Int J Cancer, 2021 Jan;148:285-295; Sandoval RL et al. PLoS One, 2021 Feb;16:e0247363). However, in one study, this variant was reported in 8/60,466 breast cancer cases as well as 17/53,461 controls (Dorling et al. N Engl J Med 2021 02;384:428-439). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 555 of the RAD50 protein (p.Ile555Val). This variant is present in population databases (rs201120953, gnomAD 0.01%). This missense change has been observed in individual(s) with breast cancer and/or pancreatic cancer (PMID: 26483394, 29785153, 32658311, 33606809). ClinVar contains an entry for this variant (Variation ID: 37379). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt RAD50 protein function with a negative predictive value of 80%. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneKor MSA | Aug 01, 2018 | - - |
Nijmegen breakage syndrome-like disorder Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 22, 2024 | - - |
Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | Sep 15, 2021 | - - |
not specified Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 22, 2021 | DNA sequence analysis of the RAD50 gene demonstrated a sequence change, c.1663A>G, in exon 11 that results in an amino acid change, p.Ile555Val. This sequence change has been described in the gnomAD database with a frequency of 0.012% in the non-Finnish European subpopulation (dbSNP rs201120953). The p.Ile555Val change affects a moderately conserved amino acid residue located in a domain of the RAD50 protein that is known to be functional. The p.Ile555Val substitution appears to be benign using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). This sequence change has been reported in individuals with pancreatic cancer who underwent germline genetic testing (PMID: 26483394). Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Ile555Val change remains unknown at this time. - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 04, 2021 | Variant summary: RAD50 c.1663A>G (p.Ile555Val) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 8e-05 in 250738 control chromosomes. The observed variant frequency is approximately 1.3 fold of the estimated maximal expected allele frequency for a pathogenic variant in RAD50 causing Hereditary Breast And Ovarian Cancer Syndrome phenotype (6.3e-05), strongly suggesting that the variant is benign. c.1663A>G has been reported in the literature in settings of multigene panel testing performed on at-least one individual from a pancreatic cancer registry who was unselected for a family history of cancer (example, Hu_2016) and in settings of multigene panel testing on individuals with breast/ovarian cancer (example, Gpoidescu_2018, Tsaousis_2019, Sandoval_2021, Akcay_2020). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome/RAD50 related cancer. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three 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 uncertain significance. Some submitters cite at-least one overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as likely benign. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jul 19, 2023 | In the published literature, this variant has been reported in individuals with breast cancer (PMID: 29785153 (2018), 32658311 (2021), 33606809 (2021)) and pancreatic cancer (PMID: 26483394 (2015)). In a large-scale breast cancer association study, the variant was observed in individuals with breast cancer as well as in unaffected controls (PMID: 33471991 (2021), see also LOVD (http://databases.lovd.nl/shared/genes/RAD50)). The frequency of this variant in the general population, 0.00012 (15/128824 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at