Genetic Variant NPIPB7:p.Pro310Pro (chr16-28456739-C-T) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001396030.1(NPIPB7):c.930G>A(p.Pro310Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00029 ( 2 hom., cov: 8)

Exomes 𝑓: 0.00032 ( 31 hom. )

Failed GnomAD Quality Control

Consequence

NPIPB7
NM_001396030.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.42

Variant links:

Genes affected

NPIPB7 (HGNC:33832): (nuclear pore complex interacting protein family member B7) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

NPIPB7 links:

ENSG00000261832 (HGNC:):

ENSG00000261832 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 16-28456739-C-T is Benign according to our data. Variant chr16-28456739-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3250560.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.42 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPIPB7	NM_001396030.1 link	c.930G>A	p.Pro310Pro	synonymous_variant	Exon 7 of 7	ENST00000452313.6	NP_001382959.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPIPB7	ENST00000452313.6 link	c.930G>A	p.Pro310Pro	synonymous_variant	Exon 7 of 7	5	NM_001396030.1	ENSP00000405348.1		O75200
ENSG00000261832	ENST00000637378.1 link	c.1092G>A	p.Pro364Pro	synonymous_variant	Exon 10 of 10	5		ENSP00000490831.1		A0A1B0GW90

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

58578

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000246

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000200

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000524

Gnomad SAS

AF:

0.000601

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000293

Gnomad OTH

AF:

0.00134

GnomAD3 exomes

AF:

0.000209

AC:

AN:

19146

Hom.:

AF XY:

0.000206

AC XY:

AN XY:

9708

show subpopulations

Gnomad AFR exome

AF:

0.000575

Gnomad AMR exome

AF:

0.000261

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000634

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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000316

AC:

172

AN:

544378

Hom.:

Cov.:

AF XY:

0.000370

AC XY:

107

AN XY:

289142

show subpopulations

Gnomad4 AFR exome

AF:

0.000796

Gnomad4 AMR exome

AF:

0.000734

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000103

Gnomad4 SAS exome

AF:

0.000531

Gnomad4 FIN exome

AF:

0.000265

Gnomad4 NFE exome

AF:

0.000200

Gnomad4 OTH exome

AF:

0.000909

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000290

AC:

AN:

58594

Hom.:

Cov.:

AF XY:

0.000289

AC XY:

AN XY:

27686

show subpopulations

Gnomad4 AFR

AF:

0.000307

Gnomad4 AMR

AF:

0.000200

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000524

Gnomad4 SAS

AF:

0.000602

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000293

Gnomad4 OTH

AF:

0.00133

Alfa

AF:

0.000590

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

NPIPB7: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

3.2

DANN

Benign

0.44

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