rs299086
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_133338.3(RAD17):c.1752-349G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,764 control chromosomes in the GnomAD database, including 17,555 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.48 ( 17555 hom., cov: 31)
Consequence
RAD17
NM_133338.3 intron
NM_133338.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.45
Publications
4 publications found
Genes affected
RAD17 (HGNC:9807): (RAD17 checkpoint clamp loader component) The protein encoded by this gene is highly similar to the gene product of Schizosaccharomyces pombe rad17, a cell cycle checkpoint gene required for cell cycle arrest and DNA damage repair in response to DNA damage. This protein shares strong similarity with DNA replication factor C (RFC), and can form a complex with RFCs. This protein binds to chromatin prior to DNA damage and is phosphorylated by the checkpoint kinase ATR following damage. This protein recruits the RAD1-RAD9-HUS1 checkpoint protein complex onto chromatin after DNA damage, which may be required for its phosphorylation. The phosphorylation of this protein is required for the DNA-damage-induced cell cycle G2 arrest, and is thought to be a critical early event during checkpoint signaling in DNA-damaged cells. Multiple alternatively spliced transcript variants of this gene, which encode four distinct protein isoforms, have been reported. Two pseudogenes, located on chromosomes 7 and 13, have been identified. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.05).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.479 AC: 72691AN: 151644Hom.: 17556 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
72691
AN:
151644
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.479 AC: 72724AN: 151764Hom.: 17555 Cov.: 31 AF XY: 0.487 AC XY: 36101AN XY: 74136 show subpopulations
GnomAD4 genome
AF:
AC:
72724
AN:
151764
Hom.:
Cov.:
31
AF XY:
AC XY:
36101
AN XY:
74136
show subpopulations
African (AFR)
AF:
AC:
17162
AN:
41392
American (AMR)
AF:
AC:
8029
AN:
15246
Ashkenazi Jewish (ASJ)
AF:
AC:
1754
AN:
3470
East Asian (EAS)
AF:
AC:
2519
AN:
5110
South Asian (SAS)
AF:
AC:
2587
AN:
4822
European-Finnish (FIN)
AF:
AC:
6165
AN:
10522
Middle Eastern (MID)
AF:
AC:
131
AN:
292
European-Non Finnish (NFE)
AF:
AC:
32853
AN:
67894
Other (OTH)
AF:
AC:
1014
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.493
Heterozygous variant carriers
0
1859
3719
5578
7438
9297
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1772
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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