6-17616164-A-G

Variant summary

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

The NM_005124.4(NUP153):ā€‹c.4361T>Cā€‹(p.Val1454Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,552 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000086 ( 0 hom., cov: 32)
Exomes š‘“: 0.0000096 ( 0 hom. )

Consequence

NUP153
NM_005124.4 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.05
Variant links:
Genes affected
NUP153 (HGNC:8062): (nucleoporin 153) Nuclear pore complexes regulate the transport of macromolecules between the nucleus and cytoplasm. They are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. Nucleoporins are glycoproteins found in nuclear pores and contain characteristic pentapeptide XFXFG repeats as well as O-linked N-acetylglucosamine residues oriented towards the cytoplasm. The protein encoded by this gene has three distinct domains: a N-terminal region containing a pore targeting and an RNA-binding domain domain, a central region containing multiple zinc finger motifs, and a C-terminal region containing multiple XFXFG repeats. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]

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=0.022462249).
BS2
High AC in GnomAd4 at 13 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NUP153NM_005124.4 linkc.4361T>C p.Val1454Ala missense_variant 22/22 ENST00000262077.3 NP_005115.2 P49790-1
NUP153NM_001278209.2 linkc.4454T>C p.Val1485Ala missense_variant 23/23 NP_001265138.1 P49790-3
NUP153NM_001278210.2 linkc.4235T>C p.Val1412Ala missense_variant 21/21 NP_001265139.1 P49790-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NUP153ENST00000262077.3 linkc.4361T>C p.Val1454Ala missense_variant 22/221 NM_005124.4 ENSP00000262077.3 P49790-1
NUP153ENST00000613258.4 linkc.4235T>C p.Val1412Ala missense_variant 21/211 ENSP00000478627.1 P49790-2
NUP153ENST00000537253.5 linkc.4454T>C p.Val1485Ala missense_variant 23/232 ENSP00000444029.1 P49790-3

Frequencies

GnomAD3 genomes
AF:
0.0000859
AC:
13
AN:
151422
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000315
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000239
AC:
6
AN:
251358
Hom.:
0
AF XY:
0.00000736
AC XY:
1
AN XY:
135854
show subpopulations
Gnomad AFR exome
AF:
0.000369
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000958
AC:
14
AN:
1461130
Hom.:
0
Cov.:
30
AF XY:
0.00000550
AC XY:
4
AN XY:
726908
show subpopulations
Gnomad4 AFR exome
AF:
0.000389
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.0000859
AC:
13
AN:
151422
Hom.:
0
Cov.:
32
AF XY:
0.0000677
AC XY:
5
AN XY:
73848
show subpopulations
Gnomad4 AFR
AF:
0.000315
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000658
Hom.:
0
Bravo
AF:
0.000162
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000330
AC:
4

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 28, 2023The c.4361T>C (p.V1454A) alteration is located in exon 22 (coding exon 22) of the NUP153 gene. This alteration results from a T to C substitution at nucleotide position 4361, causing the valine (V) at amino acid position 1454 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.42
T
BayesDel_noAF
Benign
-0.52
CADD
Benign
16
DANN
Benign
0.74
DEOGEN2
Benign
0.013
.;.;T
Eigen
Benign
-0.75
Eigen_PC
Benign
-0.67
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Benign
0.48
T;T;T
M_CAP
Benign
0.0084
T
MetaRNN
Benign
0.022
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.90
.;.;L
PrimateAI
Benign
0.36
T
PROVEAN
Benign
-1.3
.;N;N
REVEL
Benign
0.079
Sift
Benign
0.35
.;T;T
Sift4G
Benign
0.55
T;T;T
Polyphen
0.10
.;.;B
Vest4
0.17
MVP
0.30
MPC
0.036
ClinPred
0.041
T
GERP RS
3.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.045
gMVP
0.28

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs145299953; hg19: chr6-17616395; API