rs3738579
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021133.4(RNASEL):c.-95T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 1,539,808 control chromosomes in the GnomAD database, including 86,593 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 0.28 ( 6670 hom., cov: 33)
Exomes 𝑓: 0.33 ( 79923 hom. )
Consequence
RNASEL
NM_021133.4 5_prime_UTR
NM_021133.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.569
Genes affected
RNASEL (HGNC:10050): (ribonuclease L) This gene encodes a component of the interferon-regulated 2-5A system that functions in the antiviral and antiproliferative roles of interferons. The protein is involved in innate immunity and is active against multiple RNA viruses, including the influenza and SARS-CoV-2 viruses. Mutations in this gene have been associated with predisposition to prostate cancer and this gene is a candidate for the hereditary prostate cancer 1 (HPC1) allele. [provided by RefSeq, Nov 2021]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNASEL | NM_021133.4 | c.-95T>C | 5_prime_UTR_variant | 2/7 | ENST00000367559.7 | NP_066956.1 | ||
RNASEL | XM_047427096.1 | c.-95T>C | 5_prime_UTR_variant | 2/7 | XP_047283052.1 | |||
RNASEL | XM_047427106.1 | c.-95T>C | 5_prime_UTR_variant | 2/6 | XP_047283062.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNASEL | ENST00000367559.7 | c.-95T>C | 5_prime_UTR_variant | 2/7 | 1 | NM_021133.4 | ENSP00000356530.3 | |||
RNASEL | ENST00000539397.1 | c.-95T>C | 5_prime_UTR_variant | 2/6 | 2 | ENSP00000440844.1 |
Frequencies
GnomAD3 genomes AF: 0.276 AC: 41949AN: 152088Hom.: 6673 Cov.: 33
GnomAD3 genomes
AF:
AC:
41949
AN:
152088
Hom.:
Cov.:
33
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:
GnomAD4 exome AF: 0.333 AC: 462718AN: 1387602Hom.: 79923 Cov.: 22 AF XY: 0.333 AC XY: 231443AN XY: 694340
GnomAD4 exome
AF:
AC:
462718
AN:
1387602
Hom.:
Cov.:
22
AF XY:
AC XY:
231443
AN XY:
694340
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.276 AC: 41950AN: 152206Hom.: 6670 Cov.: 33 AF XY: 0.276 AC XY: 20513AN XY: 74410
GnomAD4 genome
AF:
AC:
41950
AN:
152206
Hom.:
Cov.:
33
AF XY:
AC XY:
20513
AN XY:
74410
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1004
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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