rs17166050
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005732.4(RAD50):c.551+19G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 1,597,502 control chromosomes in the GnomAD database, including 31,613 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005732.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAD50 | ENST00000378823.8 | c.551+19G>A | intron_variant | Intron 4 of 24 | 1 | NM_005732.4 | ENSP00000368100.4 | |||
ENSG00000283782 | ENST00000640655.2 | c.254+19G>A | intron_variant | Intron 5 of 25 | 5 | ENSP00000491596.2 |
Frequencies
GnomAD3 genomes AF: 0.181 AC: 27552AN: 151980Hom.: 2697 Cov.: 32
GnomAD3 exomes AF: 0.197 AC: 49412AN: 250610Hom.: 5184 AF XY: 0.202 AC XY: 27455AN XY: 135612
GnomAD4 exome AF: 0.197 AC: 284038AN: 1445404Hom.: 28912 Cov.: 31 AF XY: 0.199 AC XY: 143156AN XY: 719884
GnomAD4 genome AF: 0.181 AC: 27559AN: 152098Hom.: 2701 Cov.: 32 AF XY: 0.183 AC XY: 13623AN XY: 74350
ClinVar
Submissions by phenotype
Nijmegen breakage syndrome-like disorder Benign:3
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not provided Benign:2
Variant summary: The RAD50 c.551+19G>A variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant along with 4/5 splice site tools predicting the variant not to have an impact on splicing. This variant was found in 24021/120846 control chromosomes (2524 homozygotes) at a frequency of 0.1987736, which greatly exceeds the estimated maximal expected allele frequency of a pathogenic RAD50 variant (0.0000625), suggesting this variant is a common benign polymorphism. Taken together, this variant is classified as Benign. -
This variant is associated with the following publications: (PMID: 24093751) -
not specified Benign:1
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Familial cancer of breast Benign:1
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Hereditary cancer-predisposing syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at