rs3134945
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006913.4(RNF5):c.140+64C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 1,507,000 control chromosomes in the GnomAD database, including 33,346 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 0.18 ( 2642 hom., cov: 31)
Exomes 𝑓: 0.20 ( 30704 hom. )
Consequence
RNF5
NM_006913.4 intron
NM_006913.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.576
Genes affected
RNF5 (HGNC:10068): (ring finger protein 5) The protein encoded by this gene contains a RING finger, which is a motif known to be involved in protein-protein interactions. This protein is a membrane-bound ubiquitin ligase. It can regulate cell motility by targeting paxillin ubiquitination and altering the distribution and localization of paxillin in cytoplasm and cell focal adhesions. [provided by RefSeq, Jul 2008]
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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=-0.78).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF5 | NM_006913.4 | c.140+64C>A | intron_variant | ENST00000375094.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF5 | ENST00000375094.4 | c.140+64C>A | intron_variant | 1 | NM_006913.4 | P1 | |||
RNF5 | ENST00000487940.1 | n.215+64C>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.181 AC: 27518AN: 151776Hom.: 2645 Cov.: 31
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GnomAD4 exome AF: 0.203 AC: 275264AN: 1355106Hom.: 30704 AF XY: 0.200 AC XY: 135360AN XY: 677718
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GnomAD4 genome ? AF: 0.181 AC: 27513AN: 151894Hom.: 2642 Cov.: 31 AF XY: 0.174 AC XY: 12926AN XY: 74242
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at