GeneBe

NM_021133.4:c.2040-102A>C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_021133.4(RNASEL):​c.2040-102A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 7.7e-7 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

RNASEL
NM_021133.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.108

Publications

18 publications found
Variant links:
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]
RNASEL Gene-Disease associations (from GenCC):
  • prostate cancer, hereditary, 1
    Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RNASELNM_021133.4 linkc.2040-102A>C intron_variant Intron 6 of 6 ENST00000367559.7 NP_066956.1 Q05823-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RNASELENST00000367559.7 linkc.2040-102A>C intron_variant Intron 6 of 6 1 NM_021133.4 ENSP00000356530.3 Q05823-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
7.73e-7
AC:
1
AN:
1293806
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
646182
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
29720
American (AMR)
AF:
0.00
AC:
0
AN:
36740
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24750
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36014
South Asian (SAS)
AF:
0.00
AC:
0
AN:
78474
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
40530
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5378
European-Non Finnish (NFE)
AF:
0.00000101
AC:
1
AN:
987528
Other (OTH)
AF:
0.00
AC:
0
AN:
54672
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
3991

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.99
DANN
Benign
0.61
PhyloP100
-0.11

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs11807829; hg19: chr1-182544815; API