Genetic Variant NM_153029.4:c.*3998C>T (chr16-48538906-G-A) – ACMG Classification: Benign (-12 pts)

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

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]

N4BP1 links:

ENSG00000295475 (HGNC:):

ENSG00000295475 links:

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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
N4BP1	NM_153029.4 link	c.*3998C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000262384.4	NP_694574.3	O75113
N4BP1	XM_011523482.2 link	c.*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
N4BP1	ENST00000262384.4 link	c.*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.:

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:

AN:

Hom.:

Cov.:

AF XY:

0.350

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.313

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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.:

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

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

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

(source)

DANN

Benign

0.76

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over