dbSNP rs1292446355: NPIPB5:p.Ser255Cys (chr16-22533747-C-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001395849.1(NPIPB5):c.764C>G(p.Ser255Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0060 ( 0 hom., cov: 5)

Exomes 𝑓: 0.0078 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

NPIPB5
NM_001395849.1 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.124

Variant links:

Genes affected

NPIPB5 (HGNC:37233): (nuclear pore complex interacting protein family member B5) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

NPIPB5 links:

LOC105371131 (HGNC:):

LOC105371131 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0062442124).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPIPB5	NM_001395849.1 link	c.764C>G	p.Ser255Cys	missense_variant	Exon 7 of 7	ENST00000424340.7	NP_001382778.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPIPB5	ENST00000424340.7 link	c.764C>G	p.Ser255Cys	missense_variant	Exon 7 of 7	1	NM_001395849.1	ENSP00000440703.1		A8MRT5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

125

AN:

21050

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00288

Gnomad AMI

AF:

0.0128

Gnomad AMR

AF:

0.00565

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00528

Gnomad FIN

AF:

0.00964

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00925

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00328

AC:

AN:

21032

Hom.:

AF XY:

0.00308

AC XY:

AN XY:

11050

show subpopulations

Gnomad AFR exome

AF:

0.000866

Gnomad AMR exome

AF:

0.00235

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00561

Gnomad SAS exome

AF:

0.00480

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00336

Gnomad OTH exome

AF:

0.00146

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00780

AC:

3513

AN:

450130

Hom.:

Cov.:

AF XY:

0.00748

AC XY:

1783

AN XY:

238316

show subpopulations

Gnomad4 AFR exome

AF:

0.00273

Gnomad4 AMR exome

AF:

0.00266

Gnomad4 ASJ exome

AF:

0.000647

Gnomad4 EAS exome

AF:

0.0000647

Gnomad4 SAS exome

AF:

0.00552

Gnomad4 FIN exome

AF:

0.00964

Gnomad4 NFE exome

AF:

0.0101

Gnomad4 OTH exome

AF:

0.00626

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00601

AC:

127

AN:

21142

Hom.:

Cov.:

AF XY:

0.00628

AC XY:

AN XY:

10034

show subpopulations

Gnomad4 AFR

AF:

0.00285

Gnomad4 AMR

AF:

0.00560

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00880

Gnomad4 FIN

AF:

0.00964

Gnomad4 NFE

AF:

0.00925

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00194

Hom.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Nov 12, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.764C>G (p.S255C) alteration is located in exon 7 (coding exon 7) of the NPIPB5 gene. This alteration results from a C to G substitution at nucleotide position 764, causing the serine (S) at amino acid position 255 to be replaced by a cysteine (C). 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

0.19

BayesDel_addAF

Benign

-0.16

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Benign

0.76

DEOGEN2

Benign

0.066

.;.;T;T;.;.

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.0047

LIST_S2

Benign

0.51

.;T;T;.;T;.

M_CAP

Benign

0.0053

MetaRNN

Benign

0.0062

T;T;T;T;T;T

MetaSVM

Benign

-0.97

PROVEAN

Benign

-1.9

N;.;N;N;N;.

REVEL

Benign

0.026

Sift

Benign

0.066

T;.;T;T;T;.

Sift4G

Benign

0.070

T;D;D;D;T;T

Polyphen

0.0050

.;.;B;B;.;.

Vest4

0.14, 0.081, 0.11, 0.17

MutPred

0.49

Loss of glycosylation at S255 (P = 0.0216);Loss of glycosylation at S255 (P = 0.0216);Loss of glycosylation at S255 (P = 0.0216);Loss of glycosylation at S255 (P = 0.0216);Loss of glycosylation at S255 (P = 0.0216);.;

MVP

0.088

ClinPred

0.0027

Varity_R

0.11

gMVP

0.0071

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over