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GeneBe

rs28933996

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000326071.8(NOL4L):c.245C>T(p.Thr82Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00152 in 577,192 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/11 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0043 ( 7 hom., cov: 32)
Exomes 𝑓: 0.00054 ( 0 hom. )

Consequence

NOL4L
ENST00000326071.8 missense

Scores

1
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.169
Variant links:
Genes affected
NOL4L (HGNC:16106): (nucleolar protein 4 like) Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0033648312).
BS2
High AC in GnomAd at 640 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NOL4LNM_001256798.2 linkuse as main transcriptc.842-8587C>T intron_variant ENST00000621426.7
NOL4LNM_001351680.2 linkuse as main transcriptc.110-8587C>T intron_variant
NOL4LNM_080616.6 linkuse as main transcriptc.110-8587C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NOL4LENST00000621426.7 linkuse as main transcriptc.842-8587C>T intron_variant 5 NM_001256798.2 P1

Frequencies

GnomAD3 genomes
AF:
0.00421
AC:
640
AN:
152062
Hom.:
8
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0144
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00157
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0000882
Gnomad OTH
AF:
0.00383
GnomAD3 exomes
AF:
0.000576
AC:
26
AN:
45148
Hom.:
1
AF XY:
0.000378
AC XY:
9
AN XY:
23828
show subpopulations
Gnomad AFR exome
AF:
0.0144
Gnomad AMR exome
AF:
0.000182
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000200
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000664
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000541
AC:
230
AN:
425012
Hom.:
0
Cov.:
0
AF XY:
0.000471
AC XY:
107
AN XY:
227196
show subpopulations
Gnomad4 AFR exome
AF:
0.0155
Gnomad4 AMR exome
AF:
0.000821
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000488
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000839
Gnomad4 OTH exome
AF:
0.00177
GnomAD4 genome
AF:
0.00426
AC:
648
AN:
152180
Hom.:
7
Cov.:
32
AF XY:
0.00423
AC XY:
315
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.0146
Gnomad4 AMR
AF:
0.00157
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000882
Gnomad4 OTH
AF:
0.00379
Alfa
AF:
0.00305
Hom.:
3
Bravo
AF:
0.00483
ExAC
AF:
0.000903
AC:
18
Asia WGS
AF:
0.00115
AC:
4
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.65
T
BayesDel_noAF
Benign
-0.69
Cadd
Benign
0.16
Dann
Benign
0.45
DEOGEN2
Benign
0.034
T
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.011
N
LIST_S2
Benign
0.39
T
MetaRNN
Benign
0.0034
T
MetaSVM
Benign
-1.0
T
MutationTaster
Benign
1.0
N;N;N;N
PROVEAN
Benign
-1.9
N
REVEL
Benign
0.0050
Sift
Pathogenic
0.0
D
Polyphen
0.029
B
Vest4
0.089
MVP
0.043
ClinPred
0.0086
T
GERP RS
-0.71
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.8

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs113794459; hg19: chr20-31052785; API