chr2-10644341-C-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024894.4(NOL10):āc.1005G>Cā(p.Lys335Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000394 in 1,539,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00032 ( 0 hom., cov: 32)
Exomes š: 0.00040 ( 0 hom. )
Consequence
NOL10
NM_024894.4 missense
NM_024894.4 missense
Scores
2
8
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.82
Genes affected
NOL10 (HGNC:25862): (nucleolar protein 10) Enables RNA binding activity. Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Located in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.1190401).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOL10 | NM_024894.4 | c.1005G>C | p.Lys335Asn | missense_variant | 13/21 | ENST00000381685.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOL10 | ENST00000381685.10 | c.1005G>C | p.Lys335Asn | missense_variant | 13/21 | 1 | NM_024894.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000316 AC: 48AN: 152122Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
48
AN:
152122
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.000286 AC: 43AN: 150578Hom.: 0 AF XY: 0.000227 AC XY: 18AN XY: 79218
GnomAD3 exomes
AF:
AC:
43
AN:
150578
Hom.:
AF XY:
AC XY:
18
AN XY:
79218
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000403 AC: 559AN: 1387536Hom.: 0 Cov.: 28 AF XY: 0.000406 AC XY: 278AN XY: 684412
GnomAD4 exome
AF:
AC:
559
AN:
1387536
Hom.:
Cov.:
28
AF XY:
AC XY:
278
AN XY:
684412
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: 0.000315 AC: 48AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74420
GnomAD4 genome
AF:
AC:
48
AN:
152240
Hom.:
Cov.:
32
AF XY:
AC XY:
17
AN XY:
74420
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:
TwinsUK
AF:
AC:
2
ALSPAC
AF:
AC:
2
ESP6500AA
AF:
AC:
1
ESP6500EA
AF:
AC:
4
ExAC
AF:
AC:
30
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D;T
Sift4G
Uncertain
D;D;D;T
Polyphen
B;.;P;.
Vest4
MutPred
0.47
.;.;Loss of ubiquitination at K335 (P = 0.027);.;
MVP
MPC
0.37
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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