NM_153029.4:c.*3998C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_153029.4(N4BP1):​c.*3998C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,084 control chromosomes in the GnomAD database, including 13,599 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 0.41 ( 13592 hom., cov: 32)
Exomes 𝑓: 0.34 ( 7 hom. )

Consequence

N4BP1
NM_153029.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.03

Publications

14 publications found
Variant links:
Genes affected
N4BP1 (HGNC:29850): (NEDD4 binding protein 1) Enables mRNA binding activity; ribonuclease activity; and ubiquitin binding activity. Involved in cellular response to UV and negative regulation of viral genome replication. Predicted to be located in cytosol and nucleolus. Predicted to be active in PML body. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
N4BP1NM_153029.4 linkc.*3998C>T 3_prime_UTR_variant Exon 7 of 7 ENST00000262384.4 NP_694574.3 O75113
N4BP1XM_011523482.2 linkc.*3998C>T 3_prime_UTR_variant Exon 6 of 6 XP_011521784.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
N4BP1ENST00000262384.4 linkc.*3998C>T 3_prime_UTR_variant Exon 7 of 7 1 NM_153029.4 ENSP00000262384.3 O75113

Frequencies

GnomAD3 genomes
AF:
0.406
AC:
61719
AN:
151868
Hom.:
13570
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.576
Gnomad AMI
AF:
0.293
Gnomad AMR
AF:
0.423
Gnomad ASJ
AF:
0.301
Gnomad EAS
AF:
0.246
Gnomad SAS
AF:
0.408
Gnomad FIN
AF:
0.414
Gnomad MID
AF:
0.405
Gnomad NFE
AF:
0.318
Gnomad OTH
AF:
0.396
GnomAD4 exome
AF:
0.337
AC:
33
AN:
98
Hom.:
7
Cov.:
0
AF XY:
0.350
AC XY:
28
AN XY:
80
show subpopulations
African (AFR)
AF:
1.00
AC:
4
AN:
4
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
0.500
AC:
1
AN:
2
European-Finnish (FIN)
AF:
0.333
AC:
2
AN:
6
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.313
AC:
25
AN:
80
Other (OTH)
AF:
0.167
AC:
1
AN:
6
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.480
Heterozygous variant carriers
0
1
2
3
4
5
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
AF:
0.407
AC:
61790
AN:
151986
Hom.:
13592
Cov.:
32
AF XY:
0.410
AC XY:
30416
AN XY:
74264
show subpopulations
African (AFR)
AF:
0.575
AC:
23848
AN:
41464
American (AMR)
AF:
0.424
AC:
6475
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.301
AC:
1046
AN:
3470
East Asian (EAS)
AF:
0.246
AC:
1266
AN:
5140
South Asian (SAS)
AF:
0.406
AC:
1955
AN:
4814
European-Finnish (FIN)
AF:
0.414
AC:
4370
AN:
10552
Middle Eastern (MID)
AF:
0.395
AC:
116
AN:
294
European-Non Finnish (NFE)
AF:
0.318
AC:
21602
AN:
67948
Other (OTH)
AF:
0.400
AC:
846
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1772
3544
5316
7088
8860
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
576
1152
1728
2304
2880
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.357
Hom.:
15013
Bravo
AF:
0.415
Asia WGS
AF:
0.401
AC:
1389
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
0.027
DANN
Benign
0.76
PhyloP100
-2.0
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs1224; hg19: chr16-48572817; API