rs2069473
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002853.4(RAD1):c.308-440A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0541 in 152,304 control chromosomes in the GnomAD database, including 314 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 0.054 ( 314 hom., cov: 33)
Consequence
RAD1
NM_002853.4 intron
NM_002853.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.454
Genes affected
RAD1 (HGNC:9806): (RAD1 checkpoint DNA exonuclease) This gene encodes a component of a heterotrimeric cell cycle checkpoint complex, known as the 9-1-1 complex, that is activated to stop cell cycle progression in response to DNA damage or incomplete DNA replication. The 9-1-1 complex is recruited by RAD17 to affected sites where it may attract specialized DNA polymerases and other DNA repair effectors. Alternatively spliced transcript variants of this gene have been described. [provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD1 | NM_002853.4 | c.308-440A>G | intron_variant | ENST00000382038.7 | |||
RAD1 | NR_026591.2 | n.357-440A>G | intron_variant, non_coding_transcript_variant | ||||
TTC23L | NR_169875.1 | n.974-6112T>C | intron_variant, non_coding_transcript_variant | ||||
TTC23L | NR_169876.1 | n.1048-6112T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD1 | ENST00000382038.7 | c.308-440A>G | intron_variant | 1 | NM_002853.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0541 AC: 8238AN: 152186Hom.: 314 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0541 AC: 8241AN: 152304Hom.: 314 Cov.: 33 AF XY: 0.0547 AC XY: 4072AN XY: 74474
GnomAD4 genome
?
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AC:
8241
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152304
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33
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4072
AN XY:
74474
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Asia WGS
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227
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at