rs195434
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003958.4(RNF8):c.*2023T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 397,926 control chromosomes in the GnomAD database, including 10,313 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 0.23 ( 8018 hom., cov: 32)
Exomes 𝑓: 0.094 ( 2295 hom. )
Consequence
RNF8
NM_003958.4 3_prime_UTR
NM_003958.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.65
Genes affected
RNF8 (HGNC:10071): (ring finger protein 8) The protein encoded by this gene contains a RING finger motif and an FHA domain. This protein has been shown to interact with several class II ubiquitin-conjugating enzymes (E2), including UBE2E1/UBCH6, UBE2E2, and UBE2E3, and may act as an ubiquitin ligase (E3) in the ubiquitination of certain nuclear proteins. This protein is also known to play a role in the DNA damage response and depletion of this protein causes cell growth inhibition and cell cycle arrest. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF8 | NM_003958.4 | c.*2023T>C | 3_prime_UTR_variant | 8/8 | ENST00000373479.9 | ||
RNF8 | NM_183078.3 | c.*1929T>C | 3_prime_UTR_variant | 7/7 | |||
RNF8 | NR_046399.2 | n.3769T>C | non_coding_transcript_exon_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF8 | ENST00000373479.9 | c.*2023T>C | 3_prime_UTR_variant | 8/8 | 1 | NM_003958.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.225 AC: 34290AN: 152082Hom.: 7989 Cov.: 32
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GnomAD4 exome AF: 0.0944 AC: 23188AN: 245726Hom.: 2295 Cov.: 0 AF XY: 0.0922 AC XY: 11477AN XY: 124526
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GnomAD4 genome ? AF: 0.226 AC: 34367AN: 152200Hom.: 8018 Cov.: 32 AF XY: 0.221 AC XY: 16477AN XY: 74438
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ClinVar
Not reported inComputational scores
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Name
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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